Structure of PDB 5q13 Chain A Binding Site BS02

Receptor Information
>5q13 Chain A (length=232) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHMELTPDQQTLLHFIMDSYNKQRMPQEITNKILKEAFSAEENFLILTEM
ATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKL
PSGHSDLLEARIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVI
LSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTEL
RTFNHHHAEMLMSWRVNDHKFTPLLCEIWDVQ
Ligand information
Ligand ID9MD
InChIInChI=1S/C26H28Cl2FN3O2/c27-17-11-9-16(10-12-17)25-31-21-15-20(29)19(28)14-22(21)32(25)24(23-8-4-5-13-34-23)26(33)30-18-6-2-1-3-7-18/h9-12,14-15,18,23-24H,1-8,13H2,(H,30,33)/t23-,24-/m0/s1
InChIKeyGSCSJUCYZMUKCP-ZEQRLZLVSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Fc1cc2nc(n([C@@H]([C@@H]3CCCCO3)C(=O)NC4CCCCC4)c2cc1Cl)c5ccc(Cl)cc5
CACTVS 3.385Fc1cc2nc(n([CH]([CH]3CCCCO3)C(=O)NC4CCCCC4)c2cc1Cl)c5ccc(Cl)cc5
ACDLabs 12.01c5c2c(n(c(c1ccc(cc1)Cl)n2)C(C3CCCCO3)C(=O)NC4CCCCC4)cc(Cl)c5F
OpenEye OEToolkits 2.0.6c1cc(ccc1c2nc3cc(c(cc3n2[C@@H]([C@@H]4CCCCO4)C(=O)NC5CCCCC5)Cl)F)Cl
OpenEye OEToolkits 2.0.6c1cc(ccc1c2nc3cc(c(cc3n2C(C4CCCCO4)C(=O)NC5CCCCC5)Cl)F)Cl
FormulaC26 H28 Cl2 F N3 O2
Name(2S)-2-[6-chloro-2-(4-chlorophenyl)-5-fluoro-1H-benzimidazol-1-yl]-N-cyclohexyl-2-[(2S)-oxan-2-yl]acetamide
ChEMBL
DrugBank
ZINC
PDB chain5q13 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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PDB5q13 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)		I273 L291 M294 H298 M332 F333 R335 S336 I339 F340 L352 I356 S359 M369 Y373 M454
Binding residue
(residue number reindexed from 1)		I29 L47 M50 H54 M88 F89 R91 S92 I95 F96 L108 I112 S115 M125 Y129 M210
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.04,IC50=0.091uM
BindingDB: IC50=91nM
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:5q13, PDBe:5q13, PDBj:5q13
PDBsum5q13
PubMed29204945
UniProtQ96RI1|NR1H4_HUMAN Bile acid receptor (Gene Name=NR1H4)

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