The `opencadd.databases.klifs` module

The opencadd.databases.klifs module offers to interact with KLIFS data

locally (KLIFS data download) and
remote (KLIFS swagger API (beta))

following the same API in its local and remote modules.

In the following, the API will be demonstrated in parallel for local and remote access for the following sources of information (classes in local and remote modules):

kinases: Details on kinases
ligands: Details on ligands
drugs: Details on kinase inhibitors
bioactivities (accessible only remotely): Details on bioactivities (extracted from ChEMBL)
structures Details on structures (extracted from the PDB)
interactions: Details on kinase-ligand interactions
conformations: Details on structures’ conformation parameters such as DFG, aC-helix, p-loop
pockets: Details on a structure’s pocket residues
modified_residues: Details on a structure’s modified residues
coordinates: Coordinates for complexes, ligands, pockets, proteins, and water

[1]:

%load_ext autoreload
%autoreload 2

[2]:

import logging
from pathlib import Path

from bravado_core.exception import SwaggerMappingError
import pandas as pd
from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole

[3]:

pd.set_option("display.max_rows", 5)
pd.set_option('display.max_columns', 50)
logger = logging.getLogger("opencadd")
logger.setLevel(logging.INFO)

Set up remote and local session

Import the session setup functions setup_remote() and setup_local().

[4]:

from opencadd.databases.klifs import setup_local, setup_remote

Remote session

Set up a remote session to work with remote KLIFS data (access via the KLIFS swagger API).

[5]:

remote = setup_remote()

[6]:

remote._client

[6]:

SerializableSwaggerClient(https://dev.klifs.net/api_v2)

Local session

Set up a local session to work with local KLIFS data (access to a KLIFS download folder).

[7]:

local = setup_local("../../opencadd/tests/data/klifs")

The setup_local function will initialize a database (a pandas.DataFrame), describing the metadata of structures contained in the KLIFS download.

[8]:

local._database

[8]:

	species.klifs	structure.pdb_id	structure.alternate_model	structure.chain	ligand.expo_id	ligand_allosteric.expo_id	structure.rmsd1	structure.rmsd2	structure.qualityscore	structure.pocket	structure.resolution	structure.missing_residues	structure.missing_atoms	interaction.fingerprint	structure.fp_i	structure.fp_ii	structure.bp_i_a	structure.bp_i_b	structure.bp_ii_in	structure.bp_ii_a_in	structure.bp_ii_b_in	structure.bp_ii_out	structure.bp_ii_b	structure.bp_iii	structure.bp_iv	structure.bp_v	kinase.names	kinase.gene_name	kinase.klifs_name	kinase.family	kinase.group	ligand.name	ligand_allosteric.name	structure.dfg	structure.ac_helix	structure.filepath	structure.klifs_id	kinase.klifs_id
0	Human	3sxr	-	A	1N1	-	0.839	1.967	6.4	KELGS____VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE...	2.40	4	0	0000000000000010000001000000000000000000000000...	0.0	0.0	1.0	1.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	[BMX]	BMX	BMX	Tec	TK	N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX...	-	out-like	in	HUMAN/BMX/3sxr_chainA	3482	472
1	Human	6uuo	-	A	QH1	-	0.806	2.028	5.2	QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ...	3.29	7	61	0000000000000000000000000000000000000000000000...	0.0	0.0	1.0	1.0	1.0	1.0	0.0	0.0	0.0	0.0	0.0	0.0	[BRAF]	BRAF	BRAF	RAF	TKL	1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf...	-	in	out-like	HUMAN/BRAF/6uuo_chainA	12347	509
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
4	Human	7lht	-	A	-	ATP	10.267	15.045	4.0	KALGKGLFSMVIRITLKVVGLRILNLPHLILEYCKAKDIIRFLQQK...	3.50	0	0	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	[LRRK2]	LRRK2	LRRK2	LRRK	TKL	-	ADENOSINE-5'-TRIPHOSPHATE	out	out	HUMAN/LRRK2/7lht_chainA	13623	495
5	Human	2ogv	-	A	-	-	1.043	2.362	6.4	KTLGAGAFGKVVEVAVKMLALMSELKIMSHLGENIVNLLGALVITE...	2.70	2	0	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	[CSF1R, FMS]	CSF1R	FMS	PDGFR	TK	-	-	out	in	HUMAN/FMS/2ogv_chainA	1243	449

6 rows × 38 columns

Access information

Different sources of information are accessible via (instances of classes introduced earlier, which are initialized upon session setup):

remote.kinases or local.kinases
remote.ligands or local.ligands
remote.drugs (not available locally)
remote.bioactivities or local.bioactivities
remote.structures or local.structures
remote.interactions or local.interactions
remote.conformations (not available locally)
remote.pockets or local.pockets
remote.modified_residues (not available locally)
remote.coordinates or local.coordinates (check more details in the “Coordinates” section of this notebook)

	kinases	ligands	structures	bioactivities	interactions	pockets	drugs	conformations	modified residues
by_kinase_klifs_id	x	x	x	x	x
by_kinase_name	x	x	x
by_ligand_klifs_id		x	x	x	x
by_ligand_expo_id		x	x	x
by_structure_klifs_id			x		x	x		x	x
by_structure_pdb_id			x
all_*	x	x	x	x	x		x	x

* all_kinases, all_kinases_groups, all_kinase_families, all_ligands, all_structures, …

Kinases

Explore access to kinase information.

All kinase groups

Remote

[9]:

remote.kinases.all_kinase_groups()

[9]:

	kinase.group
0	AGC
1	CAMK
...	...
6	TK
7	TKL

8 rows × 1 columns

Local

Note: When querying all kinase groups locally, “all” refers to “all kinase groups that are locally available” and hence does not represent all existing kinase groups.

[10]:

local.kinases.all_kinase_groups()

[10]:

	kinase.group
0	TK
1	TKL

All kinase families (in a kinase group)

Remote

[11]:

remote.kinases.all_kinase_families()

[11]:

	kinase.family
0	A6
1	ABC1
...	...
142	Wnk
143	YANK

144 rows × 1 columns

[12]:

remote.kinases.all_kinase_families(groups="TK")

[12]:

	kinase.family
0	ALK
1	Abl
...	...
29	Trk
30	VEGFR

31 rows × 1 columns

[13]:

try:
    remote.kinases.all_kinase_families(groups="XXX")
except SwaggerMappingError as e:
    print(e)

Expected type to be dict for value [400, 'KLIFS error: A provided group does not exist.'] to unmarshal to a <class 'abc.Error'>.Was <class 'list'> instead.

Local

Note: When querying all kinase families locally, “all” refers to “all kinase families that are locally available” and hence does not represent all existing kinase families.

[14]:

local.kinases.all_kinase_families()

[14]:

	kinase.family
0	Tec
1	RAF
2	Abl
3	LRRK
4	PDGFR

[15]:

local.kinases.all_kinase_families(groups="TK")

[15]:

	kinase.family
0	Tec
1	Abl
2	PDGFR

[16]:

try:
    local.kinases.all_kinase_families("XXX")
except ValueError as e:
    print(e)

Input values yield no results.

All kinase names

Remote

[17]:

remote.kinases.all_kinases()

[17]:

	kinase.klifs_id	kinase.klifs_name	kinase.full_name	kinase.gene_name	kinase.uniprot	species.klifs
0	529	A6	0		0	Mouse
1	530	A6r	0		0	Mouse
...	...	...	...	...	...	...
1125	1062	ZAP70	zeta-chain (TCR) associated protein kinase	Zap70	P43404	Mouse
1126	471	ZAP70	zeta chain of T cell receptor associated prote...	ZAP70	P43403	Human

1127 rows × 6 columns

[18]:

remote.kinases.all_kinases(groups="TK", families="Tec", species="Mouse")

[18]:

	kinase.klifs_id	kinase.klifs_name	kinase.full_name	kinase.gene_name	kinase.uniprot	species.klifs
0	574	BMX	BMX non-receptor tyrosine kinase	Bmx	P97504	Mouse
1	583	BTK	Bruton agammaglobulinemia tyrosine kinase	Btk	P35991	Mouse
2	739	ITK	IL2 inducible T cell kinase	Itk	Q03526	Mouse
3	1008	TEC	tec protein tyrosine kinase	Tec	P24604	Mouse
4	1039	TXK	TXK tyrosine kinase	Txk	P42682	Mouse

[19]:

try:
    remote.kinases.all_kinases(groups="XXX")
except SwaggerMappingError as e:
    print(e)

Expected type to be dict for value [400, 'KLIFS error: A provided group does not exist.'] to unmarshal to a <class 'abc.Error'>.Was <class 'list'> instead.

Local

Note: When querying all kinase names locally, “all” refers to “all kinase names that are locally available” and hence does not represent all existing kinase names.

[20]:

local.kinases.all_kinases(families="Tec")

[20]:

	kinase.klifs_id	kinase.klifs_name	kinase.full_name	kinase.gene_name	kinase.uniprot	species.klifs
0	472	BMX	<NA>	BMX	<NA>	Human

[21]:

local.kinases.all_kinases(families="Abl", species="Mouse")

[21]:

	kinase.klifs_id	kinase.klifs_name	kinase.full_name	kinase.gene_name	kinase.uniprot	species.klifs
0	532	ABL1	<NA>	Abl1	<NA>	Mouse

[22]:

try:
    local.kinases.all_kinases(groups="XXX")
except ValueError as e:
    print(e)

Input values yield no results.

Kinase by kinase KLIFS ID

Remote

[23]:

remote.kinases.by_kinase_klifs_id(1)

[23]:

	kinase.klifs_id	kinase.klifs_name	kinase.full_name	kinase.gene_name	kinase.family	kinase.group	kinase.subfamily	species.klifs	kinase.uniprot	kinase.iuphar	kinase.pocket
0	1	AKT1	v-akt murine thymoma viral oncogene homolog 1	AKT1	Akt	AGC		Human	P31749	1479	KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME...

[24]:

remote.kinases.by_kinase_klifs_id([1,2,10000])

[24]:

	kinase.klifs_id	kinase.klifs_name	kinase.full_name	kinase.gene_name	kinase.family	kinase.group	kinase.subfamily	species.klifs	kinase.uniprot	kinase.iuphar	kinase.pocket
0	1	AKT1	v-akt murine thymoma viral oncogene homolog 1	AKT1	Akt	AGC		Human	P31749	1479	KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME...
1	2	AKT2	v-akt murine thymoma viral oncogene homolog 2	AKT2	Akt	AGC		Human	P31751	1480	KLLGKGTFGKVILYAMKILHTVTESRVLQNTRPFLTALKYACFVME...

[25]:

try:
    remote.kinases.by_kinase_klifs_id(10000)
except SwaggerMappingError as e:
    print(e)

Expected type to be dict for value [400, 'KLIFS error: An unknown kinase ID was provided'] to unmarshal to a <class 'abc.Error'>.Was <class 'list'> instead.

Local

[26]:

local.kinases.by_kinase_klifs_id(472)

[26]:

	kinase.klifs_id	kinase.klifs_name	kinase.full_name	kinase.gene_name	kinase.family	kinase.group	kinase.subfamily	species.klifs	kinase.uniprot	kinase.iuphar	kinase.pocket
0	472	BMX	<NA>	BMX	Tec	TK	<NA>	Human	<NA>	<NA>	<NA>

[27]:

local.kinases.by_kinase_klifs_id([472, 509, 10000])

[27]:

	kinase.klifs_id	kinase.klifs_name	kinase.full_name	kinase.gene_name	kinase.family	kinase.group	kinase.subfamily	species.klifs	kinase.uniprot	kinase.iuphar	kinase.pocket
0	472	BMX	<NA>	BMX	Tec	TK	<NA>	Human	<NA>	<NA>	<NA>
1	509	BRAF	<NA>	BRAF	RAF	TKL	<NA>	Human	<NA>	<NA>	<NA>

[28]:

try:
    local.kinases.by_kinase_klifs_id(10000)
except ValueError as e:
    print(e)

Input values yield no results.

Kinase by kinase name (and species)

Remote

[29]:

remote.kinases.by_kinase_name("BMX")

[29]:

	kinase.klifs_id	kinase.klifs_name	kinase.full_name	kinase.gene_name	kinase.family	kinase.group	kinase.subfamily	species.klifs	kinase.uniprot	kinase.iuphar	kinase.pocket
0	574	BMX	BMX non-receptor tyrosine kinase	Bmx	Tec	TK		Mouse	P97504	0	KELGNGQFGVVQLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE...
1	472	BMX	BMX non-receptor tyrosine kinase	BMX	Tec	TK		Human	P51813	1942	KELGSGQFGVVQLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE...

[30]:

remote.kinases.by_kinase_name("Bmx")

[30]:

	kinase.klifs_id	kinase.klifs_name	kinase.full_name	kinase.gene_name	kinase.family	kinase.group	kinase.subfamily	species.klifs	kinase.uniprot	kinase.iuphar	kinase.pocket
0	574	BMX	BMX non-receptor tyrosine kinase	Bmx	Tec	TK		Mouse	P97504	0	KELGNGQFGVVQLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE...
1	472	BMX	BMX non-receptor tyrosine kinase	BMX	Tec	TK		Human	P51813	1942	KELGSGQFGVVQLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE...

[31]:

try:
    remote.kinases.by_kinase_name("BMX", species="Dog")
except SwaggerMappingError as e:
    print(e)

Expected type to be dict for value [400, 'KLIFS error: The provided species does not exist. '] to unmarshal to a <class 'abc.Error'>.Was <class 'list'> instead.

[32]:

remote.kinases.by_kinase_name(["BMX", "BRAF", "XXX"], species="Human")

[32]:

	kinase.klifs_id	kinase.klifs_name	kinase.full_name	kinase.gene_name	kinase.family	kinase.group	kinase.subfamily	species.klifs	kinase.uniprot	kinase.iuphar	kinase.pocket
0	509	BRAF	B-Raf proto-oncogene, serine/threonine kinase	BRAF	RAF	TKL	RAF	Human	P15056	1943	QRIGSGSFGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ...
1	472	BMX	BMX non-receptor tyrosine kinase	BMX	Tec	TK		Human	P51813	1942	KELGSGQFGVVQLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE...

Local

[33]:

local.kinases.by_kinase_name("BMX")

[33]:

	kinase.klifs_id	kinase.klifs_name	kinase.full_name	kinase.gene_name	kinase.family	kinase.group	kinase.subfamily	species.klifs	kinase.uniprot	kinase.iuphar	kinase.pocket
0	472	BMX	<NA>	BMX	Tec	TK	<NA>	Human	<NA>	<NA>	<NA>

[34]:

try:
    local.kinases.by_kinase_name("BMX", species="Dog")
except ValueError as e:
    print(e)

Input values yield no results.

[35]:

local.kinases.by_kinase_name(["BMX", "BRAF", "XXX"], species="Human")

[35]:

	kinase.klifs_id	kinase.klifs_name	kinase.full_name	kinase.gene_name	kinase.family	kinase.group	kinase.subfamily	species.klifs	kinase.uniprot	kinase.iuphar	kinase.pocket
0	472	BMX	<NA>	BMX	Tec	TK	<NA>	Human	<NA>	<NA>	<NA>
1	509	BRAF	<NA>	BRAF	RAF	TKL	<NA>	Human	<NA>	<NA>	<NA>

Ligands

Explore access to ligand information.

All ligands

Remote

[36]:

remote.ligands.all_ligands()

[36]:

	ligand.klifs_id	ligand.expo_id	ligand.name	ligand.smiles	ligand.inchikey
0	1	IHZ	5-[(2-methyl-5-{[3-(trifluoromethyl)phenyl]car...	FC(F)(F)c1cc(NC(=O)c2cc(Nc3cncc(c3)C(=O)N)c(cc...	SAAYRHKJHDIDPH-UHFFFAOYSA-N
1	2	477	3-{2-[5-(difluoromethyl)-2H-thieno[3,2-c]pyraz...	S1C=2C(=NNC2C=C1C(F)F)C=3Nc4c(ccc(c4)C(O)(CC)C...	CQZZZUNOWZUNNG-UHFFFAOYSA-N
...	...	...	...	...	...
3810	4099	0CI	5-(1-{[(3S)-1-propanoylpyrrolidin-3-yl]oxy}iso...	CCC(=O)N1CC[C@@H](C1)Oc2c3ccccc3cc(n2)C4=NNC(=...	HTXPJYDZXSMZTC-LBPRGKRZSA-N
3811	4100	VK5	~{N}-[[3-[4-[(dimethylamino)methyl]phenyl]imid...	Cc1cc(cnc1c2nnc(o2)N(C)Cc3ccc4ncc(n4c3)c5ccc(c...	CZIXXCVLEHVEBZ-UHFFFAOYSA-N

3812 rows × 5 columns

Local

Note: When querying all ligands locally, “all” refers to “all ligands that are locally available” and hence does not represent all existing ligands.

[37]:

local.ligands.all_ligands()

[37]:

	ligand.klifs_id	ligand.expo_id	ligand.name	ligand.smiles	ligand.inchikey
0	<NA>	1N1	N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX...	<NA>	<NA>
1	<NA>	QH1	1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf...	<NA>	<NA>
2	<NA>	PRC	N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]...	<NA>	<NA>
3	<NA>	-	-	<NA>	<NA>

Locally, information on SMILES and InChI keys is not available. Also no ligand ID, but maybe the KLIFS maintainers can change that?

Ligands from kinase KLIFS ID(s)

Remote

[38]:

remote.ligands.by_kinase_klifs_id(472)

[38]:

	ligand.klifs_id	ligand.expo_id	ligand.name	ligand.smiles	ligand.inchikey	kinase.klifs_id (query)
0	281	1N1	N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX...	Clc1c(NC(=O)C=2SC(=NC2)Nc3nc(nc(N4CCN(CCO)CC4)...	ZBNZXTGUTAYRHI-UHFFFAOYSA-N	472
1	632	PP2	1-TERT-BUTYL-3-(4-CHLORO-PHENYL)-1H-PYRAZOLO[3...	Clc1ccc(cc1)C2=[NH+]N(c3ncnc(N)c32)C(C)(C)C	PBBRWFOVCUAONR-UHFFFAOYSA-O	472
2	3716	H88	~{N}-[2-methyl-5-[8-[4-(methylsulfonylamino)ph...	S(=O)(=O)(Nc1ccc(c2cc3ncc4c(N(c5cc(NC(=O)CCO)c...	InChI not available	472

[39]:

remote.ligands.by_kinase_klifs_id([472, 509, 10000])

There was (were) 1/3 failed request(s).
Show error messages (up to 5 messages only):
Error for 10000: Expected type to be dict for value [400, 'KLIFS error: The provided kinase ID(s) is/are invalid'] to unmarshal to a <class 'abc.Error'>.Was <class 'list'> instead.

[39]:

	ligand.klifs_id	ligand.expo_id	ligand.name	ligand.smiles	ligand.inchikey	kinase.klifs_id (query)
0	281	1N1	N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX...	Clc1c(NC(=O)C=2SC(=NC2)Nc3nc(nc(N4CCN(CCO)CC4)...	ZBNZXTGUTAYRHI-UHFFFAOYSA-N	472
1	632	PP2	1-TERT-BUTYL-3-(4-CHLORO-PHENYL)-1H-PYRAZOLO[3...	Clc1ccc(cc1)C2=[NH+]N(c3ncnc(N)c32)C(C)(C)C	PBBRWFOVCUAONR-UHFFFAOYSA-O	472
...	...	...	...	...	...	...
68	4028	VQP	N-(3,3-dimethylbutyl)-N'-{2-fluoro-5-[(5-...	Fc1c(Nc2c(cc(F)c(NC(=O)NCCC(C)(C)C)c2)C)ccc3N=...	InChI not available	509
69	4029	V5J	3-(2-cyanopropan-2-yl)-N-[2-fluoro-4-methyl-5-...	Fc1c(NC(=O)c2cc(ccc2)C(C#N)(C)C)cc(c3cnc4c(c3)...	InChI not available	509

70 rows × 6 columns

[40]:

try:
    remote.ligands.by_kinase_klifs_id(10000)
except SwaggerMappingError as e:
    print(e)

There was (were) 1/1 failed request(s).
Show error messages (up to 5 messages only):
Error for 10000: Expected type to be dict for value [400, 'KLIFS error: The provided kinase ID(s) is/are invalid'] to unmarshal to a <class 'abc.Error'>.Was <class 'list'> instead.

Input values yield no results.

Local

[41]:

local.ligands.by_kinase_klifs_id(472)

[41]:

	ligand.klifs_id	ligand.expo_id	ligand.name	ligand.smiles	ligand.inchikey	kinase.klifs_id (query)
0	<NA>	1N1	N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX...	<NA>	<NA>	472

[42]:

local.ligands.by_kinase_klifs_id([472, 509, 10000])

[42]:

	ligand.klifs_id	ligand.expo_id	ligand.name	ligand.smiles	ligand.inchikey	kinase.klifs_id (query)
0	<NA>	1N1	N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX...	<NA>	<NA>	472
1	<NA>	QH1	1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf...	<NA>	<NA>	509

[43]:

try:
    local.ligands.by_kinase_klifs_id(10000)
except ValueError as e:
    print(e)

Input values yield no results.

Ligands from kinase name(s)

Remote

[44]:

remote.ligands.by_kinase_name(["ABL1", "BMX"])

There was (were) 1/4 failed request(s).
Show error messages (up to 5 messages only):
Error for 574: Expected type to be dict for value [400, 'KLIFS error: The provided kinase ID(s) is/are invalid'] to unmarshal to a <class 'abc.Error'>.Was <class 'list'> instead.

[44]:

	ligand.klifs_id	ligand.expo_id	ligand.name	ligand.smiles	ligand.inchikey	kinase.klifs_id (query)	kinase.klifs_name (query)	kinase.gene_name (query)	species.klifs (query)
0	281	1N1	N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX...	Clc1c(NC(=O)C=2SC(=NC2)Nc3nc(nc(N4CCN(CCO)CC4)...	ZBNZXTGUTAYRHI-UHFFFAOYSA-N	472	BMX	BMX	Human
1	632	PP2	1-TERT-BUTYL-3-(4-CHLORO-PHENYL)-1H-PYRAZOLO[3...	Clc1ccc(cc1)C2=[NH+]N(c3ncnc(N)c32)C(C)(C)C	PBBRWFOVCUAONR-UHFFFAOYSA-O	472	BMX	BMX	Human
...	...	...	...	...	...	...	...	...	...
45	3247	FYH	3-(morpholin-4-ylmethyl)-~{N}-[4-(trifluoromet...	FC(F)(F)Oc1ccc(NC(=O)c2cc(ccc2)CN3CCOCC3)cc1	MYWULUKAXYAFSH-UHFFFAOYSA-N	532	ABL1	Abl1	Mouse
46	3255	FYW	6-[(3~{R})-3-oxidanylpyrrolidin-1-yl]-5-pyrimi...	c1cc(ccc1NC(=O)c2cc(c(nc2)N3CC[C@H](C3)O)c4cnc...	LARFZNXVNANWFD-MRXNPFEDSA-N	532	ABL1	Abl1	Mouse

47 rows × 9 columns

[45]:

try:
    remote.ligands.by_kinase_name("XXX")
except SwaggerMappingError as e:
    print(e)

Expected type to be dict for value [400, 'KLIFS error: An unknown kinase name was provided'] to unmarshal to a <class 'abc.Error'>.Was <class 'list'> instead.

Local

[46]:

local.ligands.by_kinase_name(["ABL1", "BMX"])

[46]:

	ligand.klifs_id	ligand.expo_id	ligand.name	ligand.smiles	ligand.inchikey	kinase.klifs_name (query)	kinase.gene_name (query)	species.klifs (query)
0	<NA>	1N1	N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX...	<NA>	<NA>	BMX	BMX	Human
1	<NA>	PRC	N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]...	<NA>	<NA>	ABL1	Abl1	Mouse

[47]:

try:
    local.ligands.by_kinase_name("XXX")
except ValueError as e:
    print(e)

Input values yield no results.

Ligands from ligand KLIFS ID(s)

Remote

[48]:

remote.ligands.by_ligand_klifs_id([100, 200, 10000])

[48]:

	ligand.klifs_id	ligand.expo_id	ligand.name	ligand.smiles	ligand.inchikey
0	100	KSA	K-252A	O=C(OC)[C@]1(O)[C@@]2(O[C@@H](N3c4c5N2c6c(c5c7...	KOZFSFOOLUUIGY-SOLYNIJKSA-N
1	200	TSK	3-(5-fluoro-6-iodo-1-methyl-1H-indol-3-yl)-4-(...	Ic1c(F)cc2c(N(C=C2C=3C(=O)NC(=O)C3C=4c5c(OC4)c...	JBKILIGSDAQHSL-UHFFFAOYSA-N

[49]:

try:
    remote.ligands.by_ligand_klifs_id(10000)
except ValueError as e:
    print(e)

Input values yield no results.

Local

Not implemented yet.

Ligands from ligand expo ID(s)

Remote

[50]:

remote.ligands.by_ligand_expo_id(["STI", "STU", "XXX"])

[50]:

	ligand.klifs_id	ligand.expo_id	ligand.name	ligand.smiles	ligand.inchikey
0	28	STU	STAUROSPORINE	O=C1NCc2c3c4N(c5c3cccc5)[C@]6(O[C@@H](N7c4c(c8...	HKSZLNNOFSGOKW-FYTWVXJKSA-N
1	48	STI	4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-...	O=C(Nc1cc(Nc2nc(c3cnccc3)ccn2)c(cc1)C)c4ccc(cc...	KTUFNOKKBVMGRW-UHFFFAOYSA-N

[51]:

try:
    remote.ligands.by_ligand_expo_id("XXX")
except ValueError as e:
    print(e)

Input values yield no results.

Local

[52]:

local.ligands.by_ligand_expo_id(["STI", "STU", "PRC"])  # TODO why do STI STU work but XXX does not?

[52]:

	ligand.klifs_id	ligand.expo_id	ligand.name	ligand.smiles	ligand.inchikey
0	<NA>	PRC	N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]...	<NA>	<NA>

[53]:

try:
    local.ligands.by_ligand_expo_id("XXX")
except ValueError as e:
    print(e)

Input values yield no results.

Drugs

KLIFS also provides a list of approved drugs:

The drug list endpoint returns a list of all annotated kinase ligands that are either approved or are/have been in clinical trials. This information is primarily powered by the PKIDB and complemented with KLIFS curation and annotation + manually curated data from other sources (e.g. approved INNs).

https://dev.klifs.net/swagger_v2/#/Ligands/get_drug_list

Note: Only available remotely (not locally).

All drugs

Remote

[54]:

remote.drugs.all_drugs()

[54]:

	drug.inn	drug.brand_name	drug.synonym	drug.phase	drug.approval_year	drug.smiles	ligand.chembl_id	ligand.expo_id
0	Abemaciclib	['Verzenio', 'Verzenios']	ABEMACICLIB LY-2835219 LY2835219 VERZENIO VERZ...	4	2017	CCN1CCN(CC1)Cc2ccc(nc2)Nc3ncc(c(n3)c4cc5c(c(c4...	CHEMBL3301610	6ZV
1	Abivertinib	[]	A610 ABIVERTINIB AC-0010 AC0010 ACEA100610 AVI...	3		CN1CCN(CC1)c2ccc(cc2F)Nc3nc4c(cc[nH]4)c(n3)Oc5...	CHEMBL4297865
...	...	...	...	...	...	...	...	...
422	Bezuclastinib	[]	PLX9486 CGT 9486	2		Cc1c([nH]nc1C(=O)Nc2cc3cc([nH]c3nc2)c4ccccc4)C		WEJ
423	Belumosudil	['Rezurock']	KD025 SLx2119	4	2021	CC(NC(=O)COc1cccc(c1)c1nc(Nc2ccc3c(c2)cn[nH]3)...	CHEMBL2005186

424 rows × 8 columns

Bioactivities

Explore access to bioactivity information.

All bioactivities

Remote

[55]:

# Takes a couple of minutes for all ligands, thus use only top x as show case here
bioactivities_all = remote.bioactivities.all_bioactivities(_top_n=10)
bioactivities_all

[55]:

	kinase.pref_name	kinase.uniprot	kinase.chembl_id	ligand.chembl_id	ligand.bioactivity_standard_type	ligand.bioactivity_standard_relation	ligand.bioactivity_standard_value	ligand.bioactivity_standard_units	ligand.bioactivity_pchembl_value	species.chembl
0	Discoidin domain-containing receptor 2	Q16832	CHEMBL5122	CHEMBL552425	IC50	=	18.60	nM	7.73	Homo sapiens
1	Ephrin type-B receptor 2	P29323	CHEMBL3290	CHEMBL552425	EC50	=	40.00	nM	7.40	Homo sapiens
...	...	...	...	...	...	...	...	...	...	...
540	Tyrosine-protein kinase LCK	P06239	CHEMBL258	CHEMBL3086536	Ki	=	55.00	nM	7.26	Homo sapiens
541	Tyrosine-protein kinase ITK/TSK	Q08881	CHEMBL2959	CHEMBL3263052	Ki	=	0.93	nM	9.03	Homo sapiens

542 rows × 10 columns

Local

This information is not available locally.

Bioactivities from kinase KLIFS ID(s)

Remote

[56]:

remote.bioactivities.by_kinase_klifs_id([472, 10000])

There was (were) 1/2 failed request(s).
Show error messages (up to 5 messages only):
Error for 10000: Expected type to be dict for value [400, 'KLIFS error: The provided kinase ID(s) is/are invalid'] to unmarshal to a <class 'abc.Error'>.Was <class 'list'> instead.

There was (were) 2/3 failed request(s).
Show error messages (up to 5 messages only):
Error for 632: Expected type to be dict for value [400, 'KLIFS error: This ligand is not available in ChEMBL.'] to unmarshal to a <class 'abc.Error'>.Was <class 'list'> instead.
Error for 3716: Expected type to be dict for value [400, 'KLIFS error: This ligand is not available in ChEMBL.'] to unmarshal to a <class 'abc.Error'>.Was <class 'list'> instead.

[56]:

	kinase.pref_name	kinase.uniprot	kinase.chembl_id	ligand.chembl_id	ligand.bioactivity_standard_type	ligand.bioactivity_standard_relation	ligand.bioactivity_standard_value	ligand.bioactivity_standard_units	ligand.bioactivity_pchembl_value	species.chembl
0	Activin receptor type-1	Q04771	CHEMBL5903	CHEMBL1421	Kd	=	620.00	nM	6.21	Homo sapiens
1	Activin receptor type-1	Q04771	CHEMBL5903	CHEMBL1421	Ki	=	79.43	nM	7.10	Homo sapiens
...	...	...	...	...	...	...	...	...	...	...
289	Wee1-like protein kinase 2	P0C1S8	CHEMBL5095	CHEMBL1421	Kd	=	200.00	nM	6.70	Homo sapiens
290	Wee1-like protein kinase 2	P0C1S8	CHEMBL5095	CHEMBL1421	Kd	=	481.00	nM	6.32	Homo sapiens

291 rows × 10 columns

[57]:

try:
    remote.bioactivities.by_kinase_klifs_id(10000000)
except SwaggerMappingError as e:
    print(e)

There was (were) 1/1 failed request(s).
Show error messages (up to 5 messages only):
Error for 10000000: Expected type to be dict for value [400, 'KLIFS error: The provided kinase ID(s) is/are invalid'] to unmarshal to a <class 'abc.Error'>.Was <class 'list'> instead.

Input values yield no results.

Local

This information is not available locally.

Bioactivities from ligand KLIFS ID(s)

[58]:

remote.bioactivities.by_ligand_klifs_id([100, 200, 10000])

There was (were) 1/3 failed request(s).
Show error messages (up to 5 messages only):
Error for 10000: Expected type to be dict for value [400, 'KLIFS error: Could not find a ligand with the provided ID.'] to unmarshal to a <class 'abc.Error'>.Was <class 'list'> instead.

[58]:

	kinase.pref_name	kinase.uniprot	kinase.chembl_id	ligand.chembl_id	ligand.bioactivity_standard_type	ligand.bioactivity_standard_relation	ligand.bioactivity_standard_value	ligand.bioactivity_standard_units	ligand.bioactivity_pchembl_value	species.chembl	ligand.klifs_id (query)
0	cAMP-dependent protein kinase alpha-catalytic ...	Q95J97	CHEMBL4885	CHEMBL281948	IC50	=	0.016	nM	10.80	Oryctolagus cuniculus	100
1	Myosin light chain kinase, smooth muscle	P11799	CHEMBL3062	CHEMBL281948	IC50	=	0.020	nM	10.70	Gallus gallus	100
...	...	...	...	...	...	...	...	...	...	...	...
7	Vascular endothelial growth factor receptor 2	P35968	CHEMBL279	CHEMBL281948	IC50	=	43.000	nM	7.37	Homo sapiens	100
8	Glycogen synthase kinase-3 beta	P49841	CHEMBL262	CHEMBL523435	IC50	=	247.000	nM	6.61	Homo sapiens	200

9 rows × 11 columns

[59]:

try:
    remote.bioactivities.by_ligand_klifs_id(10000)
except SwaggerMappingError as e:
    print(e)

There was (were) 1/1 failed request(s).
Show error messages (up to 5 messages only):
Error for 10000: Expected type to be dict for value [400, 'KLIFS error: Could not find a ligand with the provided ID.'] to unmarshal to a <class 'abc.Error'>.Was <class 'list'> instead.

Input values yield no results.

Local

This information is not available locally.

Structures

Explore access to structure information.

All structures

Remote

[60]:

remote.structures.all_structures()

[60]:

	structure.klifs_id	structure.pdb_id	structure.alternate_model	structure.chain	species.klifs	kinase.klifs_id	kinase.klifs_name	kinase.names	kinase.family	kinase.group	structure.pocket	ligand.expo_id	ligand_allosteric.expo_id	ligand.klifs_id	ligand_allosteric.klifs_id	ligand.name	ligand_allosteric.name	structure.dfg	structure.ac_helix	structure.resolution	structure.qualityscore	structure.missing_residues	structure.missing_atoms	structure.rmsd1	structure.rmsd2	interaction.fingerprint	structure.front	structure.gate	structure.back	structure.fp_i	structure.fp_ii	structure.bp_i_a	structure.bp_i_b	structure.bp_ii_in	structure.bp_ii_a_in	structure.bp_ii_b_in	structure.bp_ii_out	structure.bp_ii_b	structure.bp_iii	structure.bp_iv	structure.bp_v	structure.grich_distance	structure.grich_angle	structure.grich_rotation	structure.filepath	structure.curation_flag
0	10970	6hhf	-	A	Human	1	AKT1	<NA>	<NA>	<NA>	KLLGKGTFGKVILYAMKIL___________SRPFLTALKYSCFVME...	G4K	-	3345	0	<NA>	<NA>	out	na	2.9	3.2	11	0	0.961	2.358	<NA>	False	False	True	False	False	False	False	False	False	False	True	False	True	True	False	20.223200	67.835503	55.009102	<NA>	False
1	10439	6buu	B	B	Human	1	AKT1	<NA>	<NA>	<NA>	KLLGKGTFGKVILYAMKILHTLTENRVLQNSRPFLTALKYSCFVME...	-	-	0	0	<NA>	<NA>	in	in	2.4	8.0	0	0	0.776	2.091	<NA>	False	False	False	False	False	False	False	False	False	False	False	False	False	False	False	17.901100	59.594799	60.872501	<NA>	False
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
12570	9069	6bq1	-	E	Human	1096	PI4KA	<NA>	<NA>	<NA>	_PMQSAAKAPYLAAIFKVGDCRQDMLALQIIDLFVFPYRVVCGVIE...	E4S	-	2974	0	<NA>	<NA>	out-like	in	NaN	6.8	2	0	1.699	2.670	<NA>	True	True	False	False	False	True	True	False	False	False	False	False	False	False	False	18.168600	58.645401	136.503006	<NA>	False
12571	9070	6bq1	-	A	Human	1096	PI4KA	<NA>	<NA>	<NA>	_PMQSAAKAPYLAAIFKVGDCRQDMLALQIIDLFVFPYRVVCGVIE...	E4S	-	2974	0	<NA>	<NA>	out-like	in	NaN	6.8	2	0	1.704	2.676	<NA>	True	False	False	False	False	False	True	False	False	False	False	False	False	False	False	18.324301	58.963501	131.186996	<NA>	False

12572 rows × 46 columns

Local

Note: When querying all structures locally, “all” refers to “all structures that are locally available” and hence does not represent all existing structures.

[61]:

local.structures.all_structures()

[61]:

	structure.klifs_id	structure.pdb_id	structure.alternate_model	structure.chain	species.klifs	kinase.klifs_id	kinase.klifs_name	kinase.names	kinase.family	kinase.group	structure.pocket	ligand.expo_id	ligand_allosteric.expo_id	ligand.klifs_id	ligand_allosteric.klifs_id	ligand.name	ligand_allosteric.name	structure.dfg	structure.ac_helix	structure.resolution	structure.qualityscore	structure.missing_residues	structure.missing_atoms	structure.rmsd1	structure.rmsd2	interaction.fingerprint	structure.front	structure.gate	structure.back	structure.fp_i	structure.fp_ii	structure.bp_i_a	structure.bp_i_b	structure.bp_ii_in	structure.bp_ii_a_in	structure.bp_ii_b_in	structure.bp_ii_out	structure.bp_ii_b	structure.bp_iii	structure.bp_iv	structure.bp_v	structure.grich_distance	structure.grich_angle	structure.grich_rotation	structure.filepath	structure.curation_flag
0	3482	3sxr	-	A	Human	472	BMX	['BMX']	Tec	TK	KELGS____VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE...	1N1	-	<NA>	<NA>	N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX...	-	out-like	in	2.40	6.4	4	0	0.839	1.967	0000000000000010000001000000000000000000000000...	<NA>	<NA>	<NA>	False	False	True	True	False	False	False	False	False	False	False	False	NaN	NaN	NaN	HUMAN/BMX/3sxr_chainA	<NA>
1	12347	6uuo	-	A	Human	509	BRAF	['BRAF']	RAF	TKL	QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ...	QH1	-	<NA>	<NA>	1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf...	-	in	out-like	3.29	5.2	7	61	0.806	2.028	0000000000000000000000000000000000000000000000...	<NA>	<NA>	<NA>	False	False	True	True	True	True	False	False	False	False	False	False	NaN	NaN	NaN	HUMAN/BRAF/6uuo_chainA	<NA>
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
4	13623	7lht	-	A	Human	495	LRRK2	['LRRK2']	LRRK	TKL	KALGKGLFSMVIRITLKVVGLRILNLPHLILEYCKAKDIIRFLQQK...	-	ATP	<NA>	<NA>	-	ADENOSINE-5'-TRIPHOSPHATE	out	out	3.50	4.0	0	0	10.267	15.045	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	NaN	NaN	NaN	HUMAN/LRRK2/7lht_chainA	<NA>
5	1243	2ogv	-	A	Human	449	FMS	['CSF1R', 'FMS']	PDGFR	TK	KTLGAGAFGKVVEVAVKMLALMSELKIMSHLGENIVNLLGALVITE...	-	-	<NA>	<NA>	-	-	out	in	2.70	6.4	2	0	1.043	2.362	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	<NA>	NaN	NaN	NaN	HUMAN/FMS/2ogv_chainA	<NA>

6 rows × 46 columns

Structures from structure KLIFS ID(s)

Remote

[62]:

remote.structures.by_structure_klifs_id([12347, 100000])

[62]:

	structure.klifs_id	structure.pdb_id	structure.alternate_model	structure.chain	species.klifs	kinase.klifs_id	kinase.klifs_name	kinase.names	kinase.family	kinase.group	structure.pocket	ligand.expo_id	ligand_allosteric.expo_id	ligand.klifs_id	ligand_allosteric.klifs_id	ligand.name	ligand_allosteric.name	structure.dfg	structure.ac_helix	structure.resolution	structure.qualityscore	structure.missing_residues	structure.missing_atoms	structure.rmsd1	structure.rmsd2	interaction.fingerprint	structure.front	structure.gate	structure.back	structure.fp_i	structure.fp_ii	structure.bp_i_a	structure.bp_i_b	structure.bp_ii_in	structure.bp_ii_a_in	structure.bp_ii_b_in	structure.bp_ii_out	structure.bp_ii_b	structure.bp_iii	structure.bp_iv	structure.bp_v	structure.grich_distance	structure.grich_angle	structure.grich_rotation	structure.filepath	structure.curation_flag
0	12347	6uuo	-	A	Human	509	BRAF	<NA>	<NA>	<NA>	QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ...	QH1	-	3715	0	<NA>	<NA>	in	out	3.29	5.2	7	61	0.806	2.028	<NA>	True	True	True	False	False	True	True	True	True	False	False	False	False	False	False	0.0	0.0	0.0	<NA>	False

[63]:

try:
    remote.structures.by_structure_klifs_id(100000)
except SwaggerMappingError as e:
    print(e)

Expected type to be dict for value [400, 'KLIFS error: An unknown structure ID was provided'] to unmarshal to a <class 'abc.Error'>.Was <class 'list'> instead.

Local

[64]:

local.structures.by_structure_klifs_id(12347)

[64]:

	structure.klifs_id	structure.pdb_id	structure.alternate_model	structure.chain	species.klifs	kinase.klifs_id	kinase.klifs_name	kinase.names	kinase.family	kinase.group	structure.pocket	ligand.expo_id	ligand_allosteric.expo_id	ligand.klifs_id	ligand_allosteric.klifs_id	ligand.name	ligand_allosteric.name	structure.dfg	structure.ac_helix	structure.resolution	structure.qualityscore	structure.missing_residues	structure.missing_atoms	structure.rmsd1	structure.rmsd2	interaction.fingerprint	structure.front	structure.gate	structure.back	structure.fp_i	structure.fp_ii	structure.bp_i_a	structure.bp_i_b	structure.bp_ii_in	structure.bp_ii_a_in	structure.bp_ii_b_in	structure.bp_ii_out	structure.bp_ii_b	structure.bp_iii	structure.bp_iv	structure.bp_v	structure.grich_distance	structure.grich_angle	structure.grich_rotation	structure.filepath	structure.curation_flag
0	12347	6uuo	-	A	Human	509	BRAF	['BRAF']	RAF	TKL	QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ...	QH1	-	<NA>	<NA>	1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf...	-	in	out-like	3.29	5.2	7	61	0.806	2.028	0000000000000000000000000000000000000000000000...	<NA>	<NA>	<NA>	False	False	True	True	True	True	False	False	False	False	False	False	NaN	NaN	NaN	HUMAN/BRAF/6uuo_chainA	<NA>

[65]:

local.structures.by_structure_klifs_id(12347).shape

[65]:

(1, 46)

[66]:

try:
    local.structures.by_structure_klifs_id(100000)
except ValueError as e:
    print(e)

Input values yield no results.

Structures from ligand KLIFS ID(s)

Remote

[67]:

remote.structures.by_ligand_klifs_id([100, 200, 10000])

[67]:

	structure.klifs_id	structure.pdb_id	structure.alternate_model	structure.chain	species.klifs	kinase.klifs_id	kinase.klifs_name	kinase.names	kinase.family	kinase.group	structure.pocket	ligand.expo_id	ligand_allosteric.expo_id	ligand.klifs_id	ligand_allosteric.klifs_id	ligand.name	ligand_allosteric.name	structure.dfg	structure.ac_helix	structure.resolution	structure.qualityscore	structure.missing_residues	structure.missing_atoms	structure.rmsd1	structure.rmsd2	interaction.fingerprint	structure.front	structure.gate	structure.back	structure.fp_i	structure.fp_ii	structure.bp_i_a	structure.bp_i_b	structure.bp_ii_in	structure.bp_ii_a_in	structure.bp_ii_b_in	structure.bp_ii_out	structure.bp_ii_b	structure.bp_iii	structure.bp_iv	structure.bp_v	structure.grich_distance	structure.grich_angle	structure.grich_rotation	structure.filepath	structure.curation_flag
0	8735	5m5a	A	A	Human	128	MELK	<NA>	<NA>	<NA>	ETIGTGGFAKVKLVAIKIMRIKTEIEALKNLRQHICQLYHVFMVLE...	KSA	-	100	0	<NA>	<NA>	in	in	1.9	8.0	0	0	0.775	2.083	<NA>	True	False	False	False	False	False	False	False	False	False	False	False	False	False	False	14.9753	51.023800	60.378601	<NA>	False
1	8733	5m5a	B	A	Human	128	MELK	<NA>	<NA>	<NA>	ETIGTGGFAKVKLVAIKIMRIKTEIEALKNLRQHICQLYHVFMVLE...	KSA	-	100	0	<NA>	<NA>	in	in	1.9	8.0	0	0	0.775	2.083	<NA>	True	False	False	False	False	False	False	False	False	False	False	False	False	False	False	14.9753	51.023800	60.378601	<NA>	False
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
12	3317	3eqf	-	A	Human	383	MAP2K1	<NA>	<NA>	<NA>	SELGAGNGGVVFKMARKLIQIIRELQVLHECNPYIVGFYGASICME...	KSA	-	100	0	<NA>	<NA>	in	out	2.7	8.0	0	0	0.816	2.199	<NA>	True	False	False	False	False	False	False	False	False	False	False	False	False	False	False	15.1080	51.288502	69.366898	<NA>	False
13	2991	1r0p	-	A	Human	446	MET	<NA>	<NA>	<NA>	EVIGRGHFGCVYHCAVKSLQFLTEGIIMKDFSPNVLSLLGILVVLP...	KSA	-	100	0	<NA>	<NA>	in	out	1.8	8.0	0	0	0.848	2.189	<NA>	True	False	False	False	True	False	False	False	False	False	False	False	False	False	False	20.0054	66.349403	48.160198	<NA>	False

14 rows × 46 columns

[68]:

try:
    remote.structures.by_ligand_klifs_id(10000)
except ValueError as e:
    print(e)

Input values yield no results.

Local

Not implemented yet.

Structures from kinase KLIFS ID(s)

Remote

[69]:

remote.structures.by_kinase_klifs_id([472, 509, 10000])

[69]:

	structure.klifs_id	structure.pdb_id	structure.alternate_model	structure.chain	species.klifs	kinase.klifs_id	kinase.klifs_name	kinase.names	kinase.family	kinase.group	structure.pocket	ligand.expo_id	ligand_allosteric.expo_id	ligand.klifs_id	ligand_allosteric.klifs_id	ligand.name	ligand_allosteric.name	structure.dfg	structure.ac_helix	structure.resolution	structure.qualityscore	structure.missing_residues	structure.missing_atoms	structure.rmsd1	structure.rmsd2	interaction.fingerprint	structure.front	structure.gate	structure.back	structure.fp_i	structure.fp_ii	structure.bp_i_a	structure.bp_i_b	structure.bp_ii_in	structure.bp_ii_a_in	structure.bp_ii_b_in	structure.bp_ii_out	structure.bp_ii_b	structure.bp_iii	structure.bp_iv	structure.bp_v	structure.grich_distance	structure.grich_angle	structure.grich_rotation	structure.filepath	structure.curation_flag
0	3483	3sxs	-	A	Human	472	BMX	<NA>	<NA>	<NA>	KELGSGQFGVVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE...	PP2	-	632	0	<NA>	<NA>	out-like	in	1.89	8.0	0	0	0.834	2.106	<NA>	True	True	False	False	False	False	True	False	False	False	False	False	False	False	False	15.3623	50.710098	62.744400	<NA>	False
1	3481	3sxr	-	B	Human	472	BMX	<NA>	<NA>	<NA>	KEL______VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE...	1N1	-	281	0	<NA>	<NA>	out-like	in	2.40	5.6	6	0	0.839	1.946	<NA>	True	True	False	False	False	True	True	False	False	False	False	False	False	False	False	0.0000	0.000000	0.000000	<NA>	False
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
225	3126	4pp7	-	B	Human	509	BRAF	<NA>	<NA>	<NA>	QRIGSGSFGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ...	2VX	-	945	0	<NA>	<NA>	in	out	3.40	8.0	0	0	0.813	2.142	<NA>	True	True	True	True	False	True	True	True	False	False	False	False	False	False	False	17.1234	55.548302	31.851000	<NA>	False
226	3095	3d4q	-	A	Human	509	BRAF	<NA>	<NA>	<NA>	QRIGSGSFGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ...	SM5	-	249	0	<NA>	<NA>	in	in	2.80	8.0	0	0	0.779	2.120	<NA>	True	True	False	False	False	False	True	False	False	False	False	False	False	False	False	14.7287	49.465599	72.604401	<NA>	False

227 rows × 46 columns

[70]:

try:
    remote.structures.by_kinase_klifs_id(10000)
except SwaggerMappingError as e:
    print(e)

Expected type to be dict for value [400, 'KLIFS error: An unknown kinase ID was provided'] to unmarshal to a <class 'abc.Error'>.Was <class 'list'> instead.

Local

[71]:

local.structures.by_kinase_klifs_id([472, 509, 10000])

[71]:

	structure.klifs_id	structure.pdb_id	structure.alternate_model	structure.chain	species.klifs	kinase.klifs_id	kinase.klifs_name	kinase.names	kinase.family	kinase.group	structure.pocket	ligand.expo_id	ligand_allosteric.expo_id	ligand.klifs_id	ligand_allosteric.klifs_id	ligand.name	ligand_allosteric.name	structure.dfg	structure.ac_helix	structure.resolution	structure.qualityscore	structure.missing_residues	structure.missing_atoms	structure.rmsd1	structure.rmsd2	interaction.fingerprint	structure.front	structure.gate	structure.back	structure.fp_i	structure.fp_ii	structure.bp_i_a	structure.bp_i_b	structure.bp_ii_in	structure.bp_ii_a_in	structure.bp_ii_b_in	structure.bp_ii_out	structure.bp_ii_b	structure.bp_iii	structure.bp_iv	structure.bp_v	structure.grich_distance	structure.grich_angle	structure.grich_rotation	structure.filepath	structure.curation_flag
0	3482	3sxr	-	A	Human	472	BMX	['BMX']	Tec	TK	KELGS____VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE...	1N1	-	<NA>	<NA>	N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX...	-	out-like	in	2.40	6.4	4	0	0.839	1.967	0000000000000010000001000000000000000000000000...	<NA>	<NA>	<NA>	False	False	True	True	False	False	False	False	False	False	False	False	NaN	NaN	NaN	HUMAN/BMX/3sxr_chainA	<NA>
1	12347	6uuo	-	A	Human	509	BRAF	['BRAF']	RAF	TKL	QRI____FGTVYKVAVKMLAFKNEVGVLRKTRVNILLFMGYAIVTQ...	QH1	-	<NA>	<NA>	1-[4-{[1-(3-{[dihydroxy(propyl)-lambda~4~-sulf...	-	in	out-like	3.29	5.2	7	61	0.806	2.028	0000000000000000000000000000000000000000000000...	<NA>	<NA>	<NA>	False	False	True	True	True	True	False	False	False	False	False	False	NaN	NaN	NaN	HUMAN/BRAF/6uuo_chainA	<NA>

[72]:

try:
    local.structures.by_kinase_klifs_id(10000)
except ValueError as e:
    print(e)

Input values yield no results.

Structures from structure PDB ID(s)

Remote

[73]:

remote.structures.by_structure_pdb_id(["3sxr", "1fpu", "xxxx"])

[73]:

	structure.klifs_id	structure.pdb_id	structure.alternate_model	structure.chain	species.klifs	kinase.klifs_id	kinase.klifs_name	kinase.names	kinase.family	kinase.group	structure.pocket	ligand.expo_id	ligand_allosteric.expo_id	ligand.klifs_id	ligand.name	ligand_allosteric.name	structure.dfg	structure.ac_helix	structure.resolution	structure.qualityscore	structure.missing_residues	structure.missing_atoms	structure.rmsd1	structure.rmsd2	interaction.fingerprint	structure.front	structure.gate	structure.back	structure.fp_i	structure.fp_ii	structure.bp_i_a	structure.bp_i_b	structure.bp_ii_in	structure.bp_ii_a_in	structure.bp_ii_b_in	structure.bp_ii_out	structure.bp_ii_b	structure.bp_iii	structure.bp_iv	structure.bp_v	structure.grich_distance	structure.grich_angle	structure.grich_rotation	structure.filepath	structure.curation_flag
0	5705	1fpu	-	B	Mouse	532	ABL1	<NA>	<NA>	<NA>	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE...	PRC	-	1793	<NA>	<NA>	out	in	2.4	9.2	0	4	0.925	2.329	<NA>	True	True	True	False	False	False	True	False	False	False	True	False	False	False	False	15.332900	51.093899	49.228901	<NA>	False
1	5728	1fpu	-	A	Mouse	532	ABL1	<NA>	<NA>	<NA>	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE...	PRC	-	1793	<NA>	<NA>	out	in	2.4	8.8	0	8	0.925	2.319	<NA>	True	True	True	False	False	True	True	False	False	False	True	False	False	False	False	16.155399	54.140202	48.741402	<NA>	False
2	3481	3sxr	-	B	Human	472	BMX	<NA>	<NA>	<NA>	KEL______VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE...	1N1	-	281	<NA>	<NA>	out-like	in	2.4	5.6	6	0	0.839	1.946	<NA>	True	True	False	False	False	True	True	False	False	False	False	False	False	False	False	0.000000	0.000000	0.000000	<NA>	False
3	3482	3sxr	-	A	Human	472	BMX	<NA>	<NA>	<NA>	KELGS____VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE...	1N1	-	281	<NA>	<NA>	out-like	in	2.4	6.4	4	0	0.839	1.967	<NA>	True	True	False	False	False	True	True	False	False	False	False	False	False	False	False	0.000000	0.000000	0.000000	<NA>	False

[74]:

try:
    remote.structures.by_structure_pdb_id("xxxx")
except SwaggerMappingError as e:
    print(e)

Expected type to be dict for value [400, 'KLIFS error: An unknown PDB-code was provided'] to unmarshal to a <class 'abc.Error'>.Was <class 'list'> instead.

Local

[75]:

local.structures.by_structure_pdb_id(["3sxr", "1fpu", "xxxx"])

[75]:

	structure.klifs_id	structure.pdb_id	structure.alternate_model	structure.chain	species.klifs	kinase.klifs_id	kinase.klifs_name	kinase.names	kinase.family	kinase.group	structure.pocket	ligand.expo_id	ligand_allosteric.expo_id	ligand.klifs_id	ligand_allosteric.klifs_id	ligand.name	ligand_allosteric.name	structure.dfg	structure.ac_helix	structure.resolution	structure.qualityscore	structure.missing_residues	structure.missing_atoms	structure.rmsd1	structure.rmsd2	interaction.fingerprint	structure.front	structure.gate	structure.back	structure.fp_i	structure.fp_ii	structure.bp_i_a	structure.bp_i_b	structure.bp_ii_in	structure.bp_ii_a_in	structure.bp_ii_b_in	structure.bp_ii_out	structure.bp_ii_b	structure.bp_iii	structure.bp_iv	structure.bp_v	structure.grich_distance	structure.grich_angle	structure.grich_rotation	structure.filepath	structure.curation_flag
0	3482	3sxr	-	A	Human	472	BMX	['BMX']	Tec	TK	KELGS____VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE...	1N1	-	<NA>	<NA>	N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX...	-	out-like	in	2.4	6.4	4	0	0.839	1.967	0000000000000010000001000000000000000000000000...	<NA>	<NA>	<NA>	False	False	True	True	False	False	False	False	False	False	False	False	NaN	NaN	NaN	HUMAN/BMX/3sxr_chainA	<NA>
1	5728	1fpu	-	A	Mouse	532	ABL1	['Abl1', 'ABL1']	Abl	TK	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE...	PRC	-	<NA>	<NA>	N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]...	-	out	out	2.4	8.8	0	8	0.925	2.319	0000000000000010000000000000000000000000000000...	<NA>	<NA>	<NA>	False	False	True	True	False	False	False	True	False	False	False	False	NaN	NaN	NaN	MOUSE/ABL1/1fpu_chainA	<NA>
2	5705	1fpu	-	B	Mouse	532	ABL1	['Abl1', 'ABL1']	Abl	TK	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE...	PRC	-	<NA>	<NA>	N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]...	-	out	out	2.4	9.2	0	4	0.925	2.329	0000000000000010000000000000000000000000000000...	<NA>	<NA>	<NA>	False	False	False	True	False	False	False	True	False	False	False	False	NaN	NaN	NaN	MOUSE/ABL1/1fpu_chainB	<NA>

[76]:

try:
    local.structures.by_structure_pdb_id("xxxx")
except ValueError as e:
    print(e)

Input values yield no results.

Structures from ligand expo ID(s)

Remote

[77]:

remote.structures.by_ligand_expo_id(["PRC", "1N1"])  # TODO why only 1N1 result?

[77]:

	structure.klifs_id	structure.pdb_id	structure.alternate_model	structure.chain	species.klifs	kinase.klifs_id	kinase.klifs_name	kinase.names	kinase.family	kinase.group	structure.pocket	ligand.expo_id	ligand_allosteric.expo_id	ligand.klifs_id	ligand_allosteric.klifs_id	ligand.name	ligand_allosteric.name	structure.dfg	structure.ac_helix	structure.resolution	structure.qualityscore	structure.missing_residues	structure.missing_atoms	structure.rmsd1	structure.rmsd2	interaction.fingerprint	structure.front	structure.gate	structure.back	structure.fp_i	structure.fp_ii	structure.bp_i_a	structure.bp_i_b	structure.bp_ii_in	structure.bp_ii_a_in	structure.bp_ii_b_in	structure.bp_ii_out	structure.bp_ii_b	structure.bp_iii	structure.bp_iv	structure.bp_v	structure.grich_distance	structure.grich_angle	structure.grich_rotation	structure.filepath	structure.curation_flag
0	5018	3lfa	-	A	Human	249	p38a	<NA>	<NA>	<NA>	SPVGS__YGSVCAVAVKKLRTYRELRLLKHMKENVIGLLDVYLVTH...	1N1	-	281	0	<NA>	<NA>	na	in	2.10	6.1	5	15	0.765	2.173	<NA>	True	True	True	False	False	True	True	False	False	False	False	False	False	False	False	0.000000	0.000000	0.000000	<NA>	False
1	8339	5vcv	-	A	Human	334	MYT1	<NA>	<NA>	<NA>	SRLGHGSYGEVFKYAVKRSRKLAEVGSHEKVGPCCVRLEQAYLQTE...	1N1	-	281	0	<NA>	<NA>	in	in	1.92	8.0	0	0	0.775	2.104	<NA>	True	True	False	False	False	True	True	False	False	False	False	False	False	False	False	18.551800	59.874401	54.618500	<NA>	False
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
37	5814	2y6o	A	A	Mouse	668	EphA4	<NA>	<NA>	<NA>	KVIGVGEFGEVCSVAIKTLDFLSEASIMGQFDPNIIHLEGVMIITE...	1N1	-	281	0	<NA>	<NA>	in	in	1.54	8.7	3	1	0.783	2.116	<NA>	True	True	True	False	False	True	True	False	False	False	False	False	False	False	False	19.312901	61.760502	52.242401	<NA>	False
38	5774	2zva	-	A	Mouse	767	LYN	<NA>	<NA>	<NA>	KKLGAGQFGEVWMVAVKTLAFLEEANLMKTLQDKLVRLYAVYIITE...	1N1	-	281	0	<NA>	<NA>	in	in	2.60	8.0	0	0	0.780	2.099	<NA>	True	True	True	False	False	True	True	False	False	False	False	False	False	False	False	19.297100	62.362701	53.872799	<NA>	False

39 rows × 46 columns

[78]:

try:
    remote.structures.by_ligand_expo_id("XXX")
except ValueError as e:
    print(e)

Input values yield no results.

Local

[79]:

local.structures.by_ligand_expo_id(["PRC", "1N1"])

[79]:

	structure.klifs_id	structure.pdb_id	structure.alternate_model	structure.chain	species.klifs	kinase.klifs_id	kinase.klifs_name	kinase.names	kinase.family	kinase.group	structure.pocket	ligand.expo_id	ligand_allosteric.expo_id	ligand.klifs_id	ligand_allosteric.klifs_id	ligand.name	ligand_allosteric.name	structure.dfg	structure.ac_helix	structure.resolution	structure.qualityscore	structure.missing_residues	structure.missing_atoms	structure.rmsd1	structure.rmsd2	interaction.fingerprint	structure.front	structure.gate	structure.back	structure.fp_i	structure.fp_ii	structure.bp_i_a	structure.bp_i_b	structure.bp_ii_in	structure.bp_ii_a_in	structure.bp_ii_b_in	structure.bp_ii_out	structure.bp_ii_b	structure.bp_iii	structure.bp_iv	structure.bp_v	structure.grich_distance	structure.grich_angle	structure.grich_rotation	structure.filepath	structure.curation_flag
0	3482	3sxr	-	A	Human	472	BMX	['BMX']	Tec	TK	KELGS____VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE...	1N1	-	<NA>	<NA>	N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX...	-	out-like	in	2.4	6.4	4	0	0.839	1.967	0000000000000010000001000000000000000000000000...	<NA>	<NA>	<NA>	False	False	True	True	False	False	False	False	False	False	False	False	NaN	NaN	NaN	HUMAN/BMX/3sxr_chainA	<NA>
1	5728	1fpu	-	A	Mouse	532	ABL1	['Abl1', 'ABL1']	Abl	TK	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE...	PRC	-	<NA>	<NA>	N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]...	-	out	out	2.4	8.8	0	8	0.925	2.319	0000000000000010000000000000000000000000000000...	<NA>	<NA>	<NA>	False	False	True	True	False	False	False	True	False	False	False	False	NaN	NaN	NaN	MOUSE/ABL1/1fpu_chainA	<NA>
2	5705	1fpu	-	B	Mouse	532	ABL1	['Abl1', 'ABL1']	Abl	TK	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE...	PRC	-	<NA>	<NA>	N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]...	-	out	out	2.4	9.2	0	4	0.925	2.329	0000000000000010000000000000000000000000000000...	<NA>	<NA>	<NA>	False	False	False	True	False	False	False	True	False	False	False	False	NaN	NaN	NaN	MOUSE/ABL1/1fpu_chainB	<NA>

[80]:

try:
    local.structures.by_ligand_expo_id("XXX")
except ValueError as e:
    print(e)

Input values yield no results.

Structures from kinase name(s)

Remote

[81]:

remote.structures.by_kinase_name(["BMX", "ABL1"])

[81]:

	structure.klifs_id	structure.pdb_id	structure.alternate_model	structure.chain	species.klifs	kinase.klifs_id	kinase.klifs_name	kinase.names	kinase.family	kinase.group	structure.pocket	ligand.expo_id	ligand_allosteric.expo_id	ligand.klifs_id	ligand_allosteric.klifs_id	ligand.name	ligand_allosteric.name	structure.dfg	structure.ac_helix	structure.resolution	structure.qualityscore	structure.missing_residues	structure.missing_atoms	structure.rmsd1	structure.rmsd2	interaction.fingerprint	structure.front	structure.gate	structure.back	structure.fp_i	structure.fp_ii	structure.bp_i_a	structure.bp_i_b	structure.bp_ii_in	structure.bp_ii_a_in	structure.bp_ii_b_in	structure.bp_ii_out	structure.bp_ii_b	structure.bp_iii	structure.bp_iv	structure.bp_v	structure.grich_distance	structure.grich_angle	structure.grich_rotation	structure.filepath	structure.curation_flag
0	1089	2g2h	-	B	Human	392	ABL1	<NA>	<NA>	<NA>	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE...	P16	-	288	0	<NA>	<NA>	out-like	in	2.00	8.0	0	0	0.863	2.140	<NA>	True	True	False	False	False	True	True	False	False	False	False	False	False	False	False	16.691601	55.077801	1.634190	<NA>	False
1	12904	6xrg	13	A	Human	392	ABL1	<NA>	<NA>	<NA>	HKLGEGQYGEVYEVAVKTLEFLKEAAVLKEIKPNLVQLLGVYIITE...	-	-	0	0	<NA>	<NA>	out	in	NaN	7.2	0	0	0.954	2.454	<NA>	False	False	False	False	False	False	False	False	False	False	False	False	False	False	False	17.191500	62.462299	73.631599	<NA>	False
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
205	5718	3dk6	-	B	Mouse	532	ABL1	<NA>	<NA>	<NA>	HK_______EVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE...	SX7	-	1792	0	<NA>	<NA>	out-like	in	2.02	5.2	7	37	0.841	1.948	<NA>	True	False	False	False	False	False	True	False	False	False	False	False	False	False	False	0.000000	0.000000	0.000000	<NA>	False
206	5715	1m52	-	B	Mouse	532	ABL1	<NA>	<NA>	<NA>	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE...	P17	-	1798	0	<NA>	<NA>	out-like	in	2.60	8.0	0	0	0.858	2.132	<NA>	True	True	True	False	False	True	True	False	False	False	False	False	False	False	False	16.919201	55.870800	2.824450	<NA>	False

207 rows × 46 columns

[82]:

try:
    remote.structures.by_kinase_name("X")
except ValueError as e:
    print(e)

Input values yield no results.

Local

[83]:

local.structures.by_kinase_name(["BMX", "Abl1"])  # ABL1 will also work.

[83]:

	structure.klifs_id	structure.pdb_id	structure.alternate_model	structure.chain	species.klifs	kinase.klifs_id	kinase.klifs_name	kinase.names	kinase.family	kinase.group	structure.pocket	ligand.expo_id	ligand_allosteric.expo_id	ligand.klifs_id	ligand_allosteric.klifs_id	ligand.name	ligand_allosteric.name	structure.dfg	structure.ac_helix	structure.resolution	structure.qualityscore	structure.missing_residues	structure.missing_atoms	structure.rmsd1	structure.rmsd2	interaction.fingerprint	structure.front	structure.gate	structure.back	structure.fp_i	structure.fp_ii	structure.bp_i_a	structure.bp_i_b	structure.bp_ii_in	structure.bp_ii_a_in	structure.bp_ii_b_in	structure.bp_ii_out	structure.bp_ii_b	structure.bp_iii	structure.bp_iv	structure.bp_v	structure.grich_distance	structure.grich_angle	structure.grich_rotation	structure.filepath	structure.curation_flag
0	3482	3sxr	-	A	Human	472	BMX	['BMX']	Tec	TK	KELGS____VVKLVAVKMIEFFQEAQTMMKLSPKLVKFYGVYIVTE...	1N1	-	<NA>	<NA>	N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROX...	-	out-like	in	2.4	6.4	4	0	0.839	1.967	0000000000000010000001000000000000000000000000...	<NA>	<NA>	<NA>	False	False	True	True	False	False	False	False	False	False	False	False	NaN	NaN	NaN	HUMAN/BMX/3sxr_chainA	<NA>
1	5728	1fpu	-	A	Mouse	532	ABL1	['Abl1', 'ABL1']	Abl	TK	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE...	PRC	-	<NA>	<NA>	N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]...	-	out	out	2.4	8.8	0	8	0.925	2.319	0000000000000010000000000000000000000000000000...	<NA>	<NA>	<NA>	False	False	True	True	False	False	False	True	False	False	False	False	NaN	NaN	NaN	MOUSE/ABL1/1fpu_chainA	<NA>
2	5705	1fpu	-	B	Mouse	532	ABL1	['Abl1', 'ABL1']	Abl	TK	HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE...	PRC	-	<NA>	<NA>	N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]...	-	out	out	2.4	9.2	0	4	0.925	2.329	0000000000000010000000000000000000000000000000...	<NA>	<NA>	<NA>	False	False	False	True	False	False	False	True	False	False	False	False	NaN	NaN	NaN	MOUSE/ABL1/1fpu_chainB	<NA>

[84]:

try:
    local.structures.by_kinase_name("XXX")
except ValueError as e:
    print(e)

Input values yield no results.

Interactions

Explore access to interaction information.

Interaction types

Remote

[85]:

remote.interactions.interaction_types

[85]:

	interaction.id	interaction.name
0	1	Apolar contact
1	2	Aromatic face-to-face
...	...	...
5	6	Protein cation - ligand anion
6	7	Protein anion - ligand cation

7 rows × 2 columns

Local

This information is not available locally.

All interactions

Remote

[86]:

remote.interactions.all_interactions()

[86]:

	structure.klifs_id	interaction.fingerprint
0	1	0000000000000010000000000000000000000000000000...
1	3	0000000000000010000000000000000000000000000000...
...	...	...
10562	13903	0000000000000010000001000000100000000000000000...
10563	13904	0000000000000010000001000000100000000000000000...

10564 rows × 2 columns

Local

[87]:

local.interactions.all_interactions()

[87]:

	structure.klifs_id	interaction.fingerprint
0	3482	0000000000000010000001000000000000000000000000...
1	12347	0000000000000000000000000000000000000000000000...
...	...	...
4	13623	<NA>
5	1243	<NA>

6 rows × 2 columns

Interactions from structure KLIFS IDs

Remote

[88]:

remote.interactions.by_structure_klifs_id([12347, 100000])

[88]:

	structure.klifs_id	interaction.fingerprint
0	12347	0000000000000000000000000000000000000000000000...

[89]:

try:
    remote.interactions.by_structure_klifs_id(1000000)
except SwaggerMappingError as e:
    print(e)

Expected type to be dict for value [400, 'KLIFS error: An unknown structure ID was provided'] to unmarshal to a <class 'abc.Error'>.Was <class 'list'> instead.

Local

Note: When querying all interactions locally, “all” refers to “all interactions that are locally available” and hence does not represent all existing interactions.

[90]:

local.interactions.by_structure_klifs_id([12347, 100000])

[90]:

	structure.klifs_id	interaction.fingerprint
0	12347	0000000000000000000000000000000000000000000000...

[91]:

try:
    local.interactions.by_structure_klifs_id(1000000)
except ValueError as e:
    print(e)

Input values yield no results.

Interactions from ligand KLIFS IDs

Remote

[92]:

remote.interactions.by_ligand_klifs_id([100, 200, 10000])

[92]:

	structure.klifs_id	interaction.fingerprint
0	288	0000000000000010000001000000100000000000000000...
1	290	0000000000000010000001000000100000000000000000...
...	...	...
12	8733	0000000000000010000001000000100000010000000000...
13	8735	0000000000000010000001000000100000010000000000...

14 rows × 2 columns

[93]:

try:
    remote.interactions.by_ligand_klifs_id(10000)
except ValueError as e:
    print(e)

Input values yield no results.

Local

Not implemented yet.

Interactions from kinase KLIFS IDs

Remote

[94]:

remote.interactions.by_kinase_klifs_id([472, 509, 10000])

[94]:

	structure.klifs_id	interaction.fingerprint
0	3050	0000000000000000000000000000000000000000000000...
1	3051	0000000000000000000000000000000000000000000000...
...	...	...
188	13617	0000000000000010000000000000000000000000000000...
189	13618	0000000000000000000000000000000000000000000000...

190 rows × 2 columns

[95]:

try:
    remote.interactions.by_kinase_klifs_id(10000)
except SwaggerMappingError as e:
    print(e)

Expected type to be dict for value [400, 'KLIFS error: An unknown kinase ID was provided'] to unmarshal to a <class 'abc.Error'>.Was <class 'list'> instead.

Local

[96]:

local.interactions.by_kinase_klifs_id([472, 509, 10000])

[96]:

	structure.klifs_id	interaction.fingerprint	kinase.klifs_id (query)
0	3482	0000000000000010000001000000000000000000000000...	472
1	12347	0000000000000000000000000000000000000000000000...	509

[97]:

try:
    local.interactions.by_kinase_klifs_id(10000)
except ValueError as e:
    print(e)

Input values yield no results.

Structure conformations

Explore access to information about structure conformations.

Note: Only available remotely (not locally).

All conformations

[98]:

remote.conformations.all_conformations()

[98]:

	structure.dfg	structure.ac_helix	structure.ac_helix_distance	structure.aloop_rotation	structure.dfg_angle_d_f	structure.dfg_d_outer_rotation	structure.dfg_d_rotation	structure.dfg_f_outer_rotation	structure.dfg_f_rotation	structure.distance_67_82	structure.distance_67_82_out	structure.mobitz_dihedral	structure.ploop_angle	structure.ploop_distance	structure.ploop_rotation	structure.reference_distance	structure.salt_bridge_17_24	structure.klifs_id
0	out	in	17.430901	36.267700	169.220993	200.0	174.0	191.0	150.0	2.73782	5.67957	135.102997	0.000000	0.000000	0.000000	12.2806	2.810118	1.0
1	in	in	16.806101	144.018005	132.630005	336.0	315.0	18.0	340.0	-2.67273	-2.80613	79.667603	63.102798	18.746799	77.155197	12.4515	2.792458	2.0
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
12570	in	out	20.793200	149.429001	105.876999	320.0	309.0	328.0	11.0	-4.84154	-2.62350	36.074100	49.096298	14.737200	56.102001	12.1255	12.212099	13903.0
12571	in	out	20.793200	149.429001	105.876999	320.0	309.0	328.0	11.0	-4.84154	-2.62350	36.074100	49.096298	14.737200	56.102001	12.1255	12.212099	13904.0

12572 rows × 18 columns

Conformations from structure KLIFS ID

[99]:

remote.conformations.by_structure_klifs_id([12347, 100000])

[99]:

	structure.dfg	structure.ac_helix	structure.ac_helix_distance	structure.aloop_rotation	structure.dfg_angle_d_f	structure.dfg_d_outer_rotation	structure.dfg_d_rotation	structure.dfg_f_outer_rotation	structure.dfg_f_rotation	structure.distance_67_82	structure.distance_67_82_out	structure.mobitz_dihedral	structure.ploop_angle	structure.ploop_distance	structure.ploop_rotation	structure.reference_distance	structure.salt_bridge_17_24	structure.klifs_id
0	in	out	20.1875	108.766998	115.929001	335.0	302.0	345.0	32.0	-3.12182	-3.45656	95.328903	0.0	0.0	0.0	12.0781	0.0	12347.0

Pockets (structure’s pocket residues)

Explore access to pocket information.

Pocket from structure KLIFS ID

Remote

[100]:

remote.pockets.by_structure_klifs_id(12347)

[100]:

	residue.klifs_id	residue.id	residue.klifs_region_id	residue.klifs_region	residue.klifs_color
0	1	461	I.1	I	khaki
1	2	462	I.2	I	khaki
...	...	...	...	...	...
83	84	_	a.l.84	a.l	cornflowerblue
84	85	_	a.l.85	a.l	cornflowerblue

85 rows × 5 columns

[101]:

try:
    remote.pockets.by_structure_klifs_id(100000)
except SwaggerMappingError as e:
    print(e)

Expected type to be dict for value [400, 'KLIFS error: Structure not found'] to unmarshal to a <class 'abc.Error'>.Was <class 'list'> instead.

Local

[102]:

local.pockets.by_structure_klifs_id(12347)

[102]:

	residue.klifs_id	residue.id	residue.klifs_region_id	residue.klifs_region	residue.klifs_color
0	1	461	I.1	I	khaki
1	2	462	I.2	I	khaki
...	...	...	...	...	...
83	84	_	a.l.84	a.l	cornflowerblue
84	85	_	a.l.85	a.l	cornflowerblue

85 rows × 5 columns

[103]:

try:
    local.pockets.by_structure_klifs_id(100000)
except ValueError as e:
    print(e)

Input values yield no results.

Residue modifications (structure’s modified residues)

Explore access to information about residue modifications in structures.

Note: Only available remotely (not locally).

Residue modifications from structure KLIFS ID

This structure has modified residues:

[104]:

remote.modified_residues.by_structure_klifs_id(4126)

[104]:

	residue.id	residue.klifs_id	residue.klifs_region_id	residue.klifs_region	residue.modification
0	15	8	g.l.8	g.l	Phosphorylated tyrosine
1	160	NaN	-	-	Phosphorylated threonine

This structure has no modifications and will return an empty DataFrame:

[105]:

remote.modified_residues.by_structure_klifs_id(12347)

[105]:

	residue.id	residue.klifs_id	residue.klifs_region_id	residue.klifs_region	residue.modification

Coordinates

Access structure coordinates!

Entity	mol2 (default)	pdb
complex (default)	local / remote	local / remote
protein	local / remote	NaN
pocket	local / remote	local
ligand	local / remote	local
water	local	NaN
ions	local	NaN

Note: The KLIFS mol2 files contain (implicit and explicit) hydrogens, whereas the pdb files do not. Therefore, the pdb files contain less atoms as compared to the mol2 files.

[106]:

PATH_KLIFS_DOWNLOAD = Path("../../opencadd/tests/data/klifs/")

… to `DataFrame` (remotely)

… from structure KLIFS ID

[107]:

remote.coordinates.to_dataframe(12347, entity="complex", extension="mol2")  # or in short
remote.coordinates.to_dataframe(12347, entity="complex")

Suspicious residue ID: _0 (from QH1_0)
Suspicious residue ID: _0 (from QH1_0)

[107]:

	atom.id	atom.name	atom.x	atom.y	atom.z	residue.id	residue.name	residue.klifs_id	residue.klifs_region_id	residue.klifs_region	residue.klifs_color
0	1	O	-29.774200	11.386900	19.882401	901	HOH	<NA>	<NA>	NaN	NaN
1	2	H1	-28.814199	11.386900	19.882401	901	HOH	<NA>	<NA>	NaN	NaN
...	...	...	...	...	...	...	...	...	...	...	...
3602	3603	OG	-31.737301	22.113701	37.994801	722	SER	<NA>	<NA>	NaN	NaN
3603	3604	HG	-31.812500	21.593599	37.191399	722	SER	<NA>	<NA>	NaN	NaN

3604 rows × 11 columns

[108]:

df = remote.coordinates.to_dataframe(12347, entity="complex", extension="mol2")
print(f"Complex (mol2): Number of atoms: {df.shape[0]}")
df = remote.coordinates.to_dataframe(12347, entity="complex", extension="pdb")
print(f"Complex (pdb): Number of atoms: {df.shape[0]}")
df = remote.coordinates.to_dataframe(12347, entity="protein", extension="mol2")
print(f"Protein (mol2): Number of atoms: {df.shape[0]}")
df = remote.coordinates.to_dataframe(12347, entity="pocket", extension="mol2")
print(f"Pocket (mol2): Number of atoms: {df.shape[0]}")
df = remote.coordinates.to_dataframe(12347, entity="ligand", extension="mol2")
print(f"Ligand (mol2): Number of atoms: {df.shape[0]}")
del df

Suspicious residue ID: _0 (from QH1_0)

Complex (mol2): Number of atoms: 3604
Complex (pdb): Number of atoms: 1819
Protein (mol2): Number of atoms: 3552
Pocket (mol2): Number of atoms: 1156

Suspicious residue ID:  (from QH1)

Ligand (mol2): Number of atoms: 49

[109]:

try:
    remote.coordinates.to_dataframe(12347, entity="complex", extension="bla")
except ValueError as e:
    print(e)
try:
    remote.coordinates.to_dataframe(12347, entity="water")
except ValueError as e:
    print(e)

Invalid extension. Select from: pdb, mol2
Entity water is not available or not available remotely.

… to `DataFrame` (locally)

… from structure KLIFS ID

[110]:

df = local.coordinates.to_dataframe(12347, entity="complex", extension="mol2")
print(f"Complex (mol2): Number of atoms: {df.shape[0]}")
df = local.coordinates.to_dataframe(12347, entity="complex", extension="pdb")
print(f"Complex (pdb): Number of atoms: {df.shape[0]}")
df = local.coordinates.to_dataframe(12347, entity="protein", extension="mol2")
print(f"Protein (mol2): Number of atoms: {df.shape[0]}")
df = local.coordinates.to_dataframe(12347, entity="pocket", extension="mol2")
print(f"Pocket (mol2): Number of atoms: {df.shape[0]}")
df = local.coordinates.to_dataframe(12347, entity="pocket", extension="pdb")
print(f"Pocket (pdb): Number of atoms: {df.shape[0]}")
df = local.coordinates.to_dataframe(12347, entity="ligand", extension="mol2")
print(f"Ligand (mol2): Number of atoms: {df.shape[0]}")
df = local.coordinates.to_dataframe(12347, entity="ligand", extension="pdb")
print(f"Ligand (pdb): Number of atoms: {df.shape[0]}")
df = local.coordinates.to_dataframe(12347, entity="water", extension="mol2")
print(f"Water (mol2): Number of atoms: {df.shape[0]}")
del df

Suspicious residue ID: _0 (from QH1_0)

Complex (mol2): Number of atoms: 3604
Complex (pdb): Number of atoms: 1819
Protein (mol2): Number of atoms: 3552
Pocket (mol2): Number of atoms: 1156

Suspicious residue ID:  (from QH1)

Pocket (pdb): Number of atoms: 1156
Ligand (mol2): Number of atoms: 49

/home/dominique/.local/miniconda/envs/oc/lib/python3.8/site-packages/biopandas/pdb/pandas_pdb.py:403: UserWarning: No ATOM entries have been loaded. Is the input file/text in the pdb format?
  warnings.warn('No ATOM entries have been loaded. '
Suspicious residue ID:  (from HOH)

Ligand (pdb): Number of atoms: 31
Water (mol2): Number of atoms: 3

[111]:

try:
    local.coordinates.to_dataframe(12347, entity="pocket", extension="bla")
except FileNotFoundError as e:
    print(e)

File ../../opencadd/tests/data/klifs/HUMAN/BRAF/6uuo_chainA/pocket.bla does not exist.

… from file

[112]:

filepath = PATH_KLIFS_DOWNLOAD / "HUMAN/BRAF/6uuo_chainA"
df = local.coordinates.to_dataframe(filepath / "complex.mol2")
print(f"Complex (mol2): Number of atoms: {df.shape[0]}")
#df = local.coordinates.to_dataframe(filepath / "complex.pdb")
#print(f"Complex (pdb): Number of atoms: {df.shape[0]}")
df = local.coordinates.to_dataframe(filepath / "protein.mol2")
print(f"Protein (mol2): Number of atoms: {df.shape[0]}")
df = local.coordinates.to_dataframe(filepath / "pocket.mol2")
print(f"Pocket (mol2): Number of atoms: {df.shape[0]}")
df = local.coordinates.to_dataframe(filepath / "pocket.pdb")
print(f"Pocket (pdb): Number of atoms: {df.shape[0]}")
df = local.coordinates.to_dataframe(filepath / "ligand.mol2")
print(f"Ligand (mol2): Number of atoms: {df.shape[0]}")
df = local.coordinates.to_dataframe(filepath / "klifs_ligand.pdb")
print(f"Ligand (pdb): Number of atoms: {df.shape[0]}")
df = local.coordinates.to_dataframe(filepath / "water.mol2")
print(f"Water (mol2): Number of atoms: {df.shape[0]}")
del df

Suspicious residue ID: _0 (from QH1_0)

Complex (mol2): Number of atoms: 3604
Protein (mol2): Number of atoms: 3552

Suspicious residue ID:  (from QH1)

Pocket (mol2): Number of atoms: 1156
Pocket (pdb): Number of atoms: 1156

Suspicious residue ID:  (from HOH)

Ligand (mol2): Number of atoms: 49
Ligand (pdb): Number of atoms: 31
Water (mol2): Number of atoms: 3

… to `rdkit` molecule (remotely)

… from structure KLIFS ID

[113]:

remote.coordinates.to_rdkit(12347, entity="ligand", extension="mol2")

[113]:

../_images/tutorials_databases_klifs_225_0.png

[114]:

remote.coordinates.to_rdkit(12347, entity="ligand", extension="mol2", compute2d=False)

[114]:

../_images/tutorials_databases_klifs_226_0.png

[115]:

try:
    remote.coordinates.to_rdkit(12347, entity="ligand", extension="pdb")
except ValueError as e:
    print(e)

Entity ligand is not available or not available remotely.

… to `rdkit` molecule (locally)

… from structure KLIFS ID

[116]:

local.coordinates.to_rdkit(12347, entity="ligand", extension="mol2")

[116]:

../_images/tutorials_databases_klifs_230_0.png

[117]:

local.coordinates.to_rdkit(12347, entity="ligand", extension="pdb")

[117]:

../_images/tutorials_databases_klifs_231_0.png

… from file

[118]:

filepath = PATH_KLIFS_DOWNLOAD / "HUMAN/BRAF/6uuo_chainA/ligand.mol2"
local.coordinates.to_rdkit(filepath)

[118]:

../_images/tutorials_databases_klifs_233_0.png

… to mol2 file (remotely)

[119]:

filepath = remote.coordinates.to_mol2(12347, ".")
print(f"{filepath} exists? {filepath.exists()}")
filepath.unlink()
del filepath

HUMAN_BRAF_6uuo_chainA_complex.mol2 exists? True

[120]:

filepath = remote.coordinates.to_mol2(12347, ".", entity="pocket")
print(f"{filepath} exists? {filepath.exists()}")
filepath.unlink()
del filepath

HUMAN_BRAF_6uuo_chainA_pocket.mol2 exists? True

[121]:

filepath = remote.coordinates.to_mol2(12347, ".", entity="pocket", in_dir=True)
print(f"{filepath} exists? {filepath.exists()}")
filepath.unlink()
del filepath

HUMAN/BRAF/6uuo_chainA/pocket.mol2 exists? True

[122]:

try:
    remote.coordinates.to_mol2(12347, ".", entity="bla")
except ValueError as e:
    print(e)

Entity bla is not available or not available remotely.

… to pdb file (remotely)

[123]:

filepath = remote.coordinates.to_pdb(12347, ".")
print(f"{filepath} exists? {filepath.exists()}")
filepath.unlink()
del filepath

HUMAN_BRAF_6uuo_chainA_complex.pdb exists? True

[124]:

try:
    remote.coordinates.to_pdb(12347, ".", entity="ligand")
except ValueError as e:
    print(e)

Entity ligand is not available or not available remotely.

The opencadd.databases.klifs module

Set up remote and local session

Remote session

Local session

Access information

Kinases

All kinase groups

All kinase families (in a kinase group)

All kinase names

Kinase by kinase KLIFS ID

Kinase by kinase name (and species)

Ligands

All ligands

Ligands from kinase KLIFS ID(s)

Ligands from kinase name(s)

Ligands from ligand KLIFS ID(s)

Ligands from ligand expo ID(s)

Drugs

All drugs

Bioactivities

All bioactivities

Bioactivities from kinase KLIFS ID(s)

Bioactivities from ligand KLIFS ID(s)

Structures

All structures

Structures from structure KLIFS ID(s)

Structures from ligand KLIFS ID(s)

Structures from kinase KLIFS ID(s)

Structures from structure PDB ID(s)

Structures from ligand expo ID(s)

Structures from kinase name(s)

Interactions

Interaction types

All interactions

Interactions from structure KLIFS IDs

Interactions from ligand KLIFS IDs

Interactions from kinase KLIFS IDs

Structure conformations

All conformations

Conformations from structure KLIFS ID

Pockets (structure’s pocket residues)

Pocket from structure KLIFS ID

Residue modifications (structure’s modified residues)

Residue modifications from structure KLIFS ID

Coordinates

… to DataFrame (remotely)

… from structure KLIFS ID

… to DataFrame (locally)

… from structure KLIFS ID

… from file

… to rdkit molecule (remotely)

… from structure KLIFS ID

… to rdkit molecule (locally)

… from structure KLIFS ID

… from file

… to mol2 file (remotely)

… to pdb file (remotely)

The `opencadd.databases.klifs` module

… to `DataFrame` (remotely)

… to `DataFrame` (locally)

… to `rdkit` molecule (remotely)

… to `rdkit` molecule (locally)