Structure of PDB 5q0y Chain A Binding Site BS02

Receptor Information
>5q0y 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 ID9LY
InChIInChI=1S/C29H32F2N6O/c30-22-16-24-25(17-23(22)31)37(28(35-24)20-12-13-26(32-18-20)36-15-7-14-33-36)27(19-8-3-1-4-9-19)29(38)34-21-10-5-2-6-11-21/h7,12-19,21,27H,1-6,8-11H2,(H,34,38)/t27-/m0/s1
InChIKeyBAGJAPIDXZLKQM-MHZLTWQESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1cnn(c1)c2ccc(cn2)c3nc4cc(c(cc4n3C(C5CCCCC5)C(=O)NC6CCCCC6)F)F
CACTVS 3.385Fc1cc2nc(n([C@@H](C3CCCCC3)C(=O)NC4CCCCC4)c2cc1F)c5ccc(nc5)n6cccn6
OpenEye OEToolkits 2.0.6c1cnn(c1)c2ccc(cn2)c3nc4cc(c(cc4n3[C@@H](C5CCCCC5)C(=O)NC6CCCCC6)F)F
CACTVS 3.385Fc1cc2nc(n([CH](C3CCCCC3)C(=O)NC4CCCCC4)c2cc1F)c5ccc(nc5)n6cccn6
ACDLabs 12.01c6c3c(n(c(c1ccc(nc1)n2nccc2)n3)C(C4CCCCC4)C(=O)NC5CCCCC5)cc(c6F)F
FormulaC29 H32 F2 N6 O
Name(2S)-N,2-dicyclohexyl-2-{5,6-difluoro-2-[6-(1H-pyrazol-1-yl)pyridin-3-yl]-1H-benzimidazol-1-yl}acetamide
ChEMBL
DrugBank
ZINC
PDB chain5q0y 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

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PDB5q0y D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		I277 N287 L291 M294 H298 M332 F333 S336 I339 F340 I356 S359 M369 Y373 M454 L455
Binding residue
(residue number reindexed from 1)		I31 N41 L45 M48 H52 M86 F87 S90 I93 F94 I110 S113 M123 Y127 M208 L209
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.73,IC50=1.87uM
BindingDB: IC50=1870nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:5q0y, PDBe:5q0y, PDBj:5q0y
PDBsum5q0y
PubMed29204945
UniProtQ96RI1|NR1H4_HUMAN Bile acid receptor (Gene Name=NR1H4)

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