The opencadd.databases.klifs module

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

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&#039;-{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&apos;-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_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 5705 1fpu - B Mouse 532 ABL1 <NA> <NA> <NA> HKLGGGQYGEVYEVAVKTLEFLKEAAVMKEIKPNLVQLLGVYIITE... PRC - 1793 0 <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 0 <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 0 <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 0 <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.