Structure of PDB 5q18 Chain A Binding Site BS02

Receptor Information
>5q18 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 ID9MY
InChIInChI=1S/C29H35F2N3O3/c1-37-27(19-10-6-3-7-11-19)28-33-24-16-22(30)23(31)17-25(24)34(28)26(18-8-4-2-5-9-18)29(36)32-20-12-14-21(35)15-13-20/h3,6-7,10-11,16-18,20-21,26-27,35H,2,4-5,8-9,12-15H2,1H3,(H,32,36)/t20-,21-,26-,27+/m0/s1
InChIKeyJJRPVOCGGUAZIT-LKSLQULUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6COC(c1ccccc1)c2nc3cc(c(cc3n2C(C4CCCCC4)C(=O)NC5CCC(CC5)O)F)F
OpenEye OEToolkits 2.0.6CO[C@H](c1ccccc1)c2nc3cc(c(cc3n2[C@@H](C4CCCCC4)C(=O)NC5CCC(CC5)O)F)F
CACTVS 3.385CO[C@H](c1ccccc1)c2nc3cc(F)c(F)cc3n2[C@@H](C4CCCCC4)C(=O)N[C@@H]5CC[C@@H](O)CC5
ACDLabs 12.01n3(C(C(=O)NC1CCC(CC1)O)C2CCCCC2)c5cc(c(cc5nc3C(c4ccccc4)OC)F)F
CACTVS 3.385CO[CH](c1ccccc1)c2nc3cc(F)c(F)cc3n2[CH](C4CCCCC4)C(=O)N[CH]5CC[CH](O)CC5
FormulaC29 H35 F2 N3 O3
Name(2S)-2-cyclohexyl-2-{5,6-difluoro-2-[(R)-methoxy(phenyl)methyl]-1H-benzimidazol-1-yl}-N-(trans-4-hydroxycyclohexyl)acetamide
ChEMBL
DrugBank
ZINC
PDB chain5q18 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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PDB5q18 D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		I277 H298 M332 S336 F340 I356 S359 I361 M369 Y373 W458
Binding residue
(residue number reindexed from 1)		I31 H52 M86 S90 F94 I110 S113 I115 M123 Y127 W212
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.17,IC50=0.0675uM
BindingDB: IC50=67.500000nM
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:5q18, PDBe:5q18, PDBj:5q18
PDBsum5q18
PubMed29204945
UniProtQ96RI1|NR1H4_HUMAN Bile acid receptor (Gene Name=NR1H4)

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