Structure of PDB 3omk Chain A Binding Site BS02

Receptor Information
>3omk 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 IDOMK
InChIInChI=1S/C28H26ClF2N3O/c1-17-7-5-6-10-23(17)33-28(35)26(18-8-3-2-4-9-18)34-25-16-22(31)21(30)15-24(25)32-27(34)19-11-13-20(29)14-12-19/h5-7,10-16,18,26H,2-4,8-9H2,1H3,(H,33,35)/t26-/m0/s1
InChIKeyLUMVOGPLODDMEP-SANMLTNESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0Cc1ccccc1NC(=O)[C@H](C2CCCCC2)n3c4cc(c(cc4nc3c5ccc(cc5)Cl)F)F
OpenEye OEToolkits 1.7.0Cc1ccccc1NC(=O)C(C2CCCCC2)n3c4cc(c(cc4nc3c5ccc(cc5)Cl)F)F
CACTVS 3.370Cc1ccccc1NC(=O)[CH](C2CCCCC2)n3c4cc(F)c(F)cc4nc3c5ccc(Cl)cc5
CACTVS 3.370Cc1ccccc1NC(=O)[C@H](C2CCCCC2)n3c4cc(F)c(F)cc4nc3c5ccc(Cl)cc5
ACDLabs 12.01Clc5ccc(c2nc1cc(F)c(F)cc1n2C(C(=O)Nc3ccccc3C)C4CCCCC4)cc5
FormulaC28 H26 Cl F2 N3 O
Name(2S)-2-[2-(4-chlorophenyl)-5,6-difluoro-1H-benzimidazol-1-yl]-2-cyclohexyl-N-(2-methylphenyl)ethanamide
ChEMBL
DrugBank
ZINCZINC000064744163
PDB chain3omk Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3omk Optimization of a novel class of benzimidazole-based farnesoid X receptor (FXR) agonists to improve physicochemical and ADME properties
Resolution1.9 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
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:3omk, PDBe:3omk, PDBj:3omk
PDBsum3omk
PubMed21269824
UniProtQ96RI1|NR1H4_HUMAN Bile acid receptor (Gene Name=NR1H4)

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