Structure of PDB 5q1a Chain A Binding Site BS02

Receptor Information
>5q1a Chain A (length=230) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MELTPDQQTLLHFIMDSYNKQRMPQEITNKILKEAFSAEENFLILTEMAT
NHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPS
GHSDLLEARIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILS
PDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRT
FNHHHAEMLMSWRVNDHKFTPLLCEIWDVQ
Ligand information
Ligand ID9N4
InChIInChI=1S/C31H35N3O3/c1-20-11-10-12-21(2)28(20)33-31(35)29(22-13-6-5-7-14-22)34-26-16-9-8-15-25(26)32-30(34)24-18-17-23(36-3)19-27(24)37-4/h8-12,15-19,22,29H,5-7,13-14H2,1-4H3,(H,33,35)/t29-/m0/s1
InChIKeyAZPPBUOGTWKZCA-LJAQVGFWSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1ccc(c(OC)c1)c2nc3ccccc3n2[CH](C4CCCCC4)C(=O)Nc5c(C)cccc5C
ACDLabs 12.01n3c5c(n(C(C(=O)Nc1c(C)cccc1C)C2CCCCC2)c3c4ccc(cc4OC)OC)cccc5
OpenEye OEToolkits 2.0.6Cc1cccc(c1NC(=O)[C@H](C2CCCCC2)n3c4ccccc4nc3c5ccc(cc5OC)OC)C
OpenEye OEToolkits 2.0.6Cc1cccc(c1NC(=O)C(C2CCCCC2)n3c4ccccc4nc3c5ccc(cc5OC)OC)C
CACTVS 3.385COc1ccc(c(OC)c1)c2nc3ccccc3n2[C@@H](C4CCCCC4)C(=O)Nc5c(C)cccc5C
FormulaC31 H35 N3 O3
Name(2S)-2-cyclohexyl-2-[2-(2,4-dimethoxyphenyl)-1H-benzimidazol-1-yl]-N-(2,6-dimethylphenyl)acetamide
ChEMBL
DrugBank
ZINC
PDB chain5q1a Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5q1a D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		N287 L291 M294 H298 M332 F333 S336 I356 S359 M369 Y373 M454
Binding residue
(residue number reindexed from 1)		N41 L45 M48 H52 M86 F87 S90 I110 S113 M123 Y127 M208
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.02,IC50=0.0096uM
BindingDB: IC50=9.600000nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0004879 nuclear receptor activity
GO:0032052 bile acid binding
Biological Process
GO:0006355 regulation of DNA-templated transcription
GO:0038183 bile acid signaling pathway

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5q1a, PDBe:5q1a, PDBj:5q1a
PDBsum5q1a
PubMed29204945
UniProtQ96RI1|NR1H4_HUMAN Bile acid receptor (Gene Name=NR1H4)

[Back to BioLiP]