Structure of PDB 5q1d Chain A Binding Site BS02

Receptor Information
>5q1d 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 ID9ND
InChIInChI=1S/C27H24ClF2N3O/c28-19-13-11-18(12-14-19)26-32-23-15-21(29)22(30)16-24(23)33(26)25(17-7-3-1-4-8-17)27(34)31-20-9-5-2-6-10-20/h2,5-6,9-17,25H,1,3-4,7-8H2,(H,31,34)/t25-/m0/s1
InChIKeyARWUUCFDBAFWCD-VWLOTQADSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc(cc1)NC(=O)[C@H](C2CCCCC2)n3c4cc(c(cc4nc3c5ccc(cc5)Cl)F)F
CACTVS 3.385Fc1cc2nc(n([CH](C3CCCCC3)C(=O)Nc4ccccc4)c2cc1F)c5ccc(Cl)cc5
ACDLabs 12.01n3(C(C(=O)Nc1ccccc1)C2CCCCC2)c5cc(c(F)cc5nc3c4ccc(cc4)Cl)F
OpenEye OEToolkits 2.0.6c1ccc(cc1)NC(=O)C(C2CCCCC2)n3c4cc(c(cc4nc3c5ccc(cc5)Cl)F)F
CACTVS 3.385Fc1cc2nc(n([C@@H](C3CCCCC3)C(=O)Nc4ccccc4)c2cc1F)c5ccc(Cl)cc5
FormulaC27 H24 Cl F2 N3 O
Name(2S)-2-[2-(4-chlorophenyl)-5,6-difluoro-1H-benzimidazol-1-yl]-2-cyclohexyl-N-phenylacetamide
ChEMBL
DrugBank
ZINC
PDB chain5q1d 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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PDB5q1d D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
Resolution1.89 Å
Binding residue
(original residue number in PDB)		I277 N287 L291 M294 H298 M332 F333 S336 I339 F340 I356 M369 Y373
Binding residue
(residue number reindexed from 1)		I31 N41 L45 M48 H52 M86 F87 S90 I93 F94 I110 M123 Y127
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.12,IC50=0.76uM
BindingDB: IC50=760nM
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
View graph for
Biological Process
External links
PDB RCSB:5q1d, PDBe:5q1d, PDBj:5q1d
PDBsum5q1d
PubMed29204945
UniProtQ96RI1|NR1H4_HUMAN Bile acid receptor (Gene Name=NR1H4)

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