Structure of PDB 5q0p Chain A Binding Site BS02

Receptor Information
>5q0p 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 ID9LA
InChIInChI=1S/C28H25ClF2N2O3/c29-20-10-6-18(7-11-20)27-32-24-14-22(30)23(31)15-25(24)33(27)26(17-4-2-1-3-5-17)16-36-21-12-8-19(9-13-21)28(34)35/h6-15,17,26H,1-5,16H2,(H,34,35)/t26-/m1/s1
InChIKeyDLAMZHRFSSYYFX-AREMUKBSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1cc(ccc1c2nc3cc(c(cc3n2C(COc4ccc(cc4)C(=O)O)C5CCCCC5)F)F)Cl
ACDLabs 12.01n3(C(C1CCCCC1)COc2ccc(cc2)C(O)=O)c5cc(F)c(cc5nc3c4ccc(cc4)Cl)F
CACTVS 3.385OC(=O)c1ccc(OC[CH](C2CCCCC2)n3c4cc(F)c(F)cc4nc3c5ccc(Cl)cc5)cc1
OpenEye OEToolkits 2.0.6c1cc(ccc1c2nc3cc(c(cc3n2[C@H](COc4ccc(cc4)C(=O)O)C5CCCCC5)F)F)Cl
CACTVS 3.385OC(=O)c1ccc(OC[C@H](C2CCCCC2)n3c4cc(F)c(F)cc4nc3c5ccc(Cl)cc5)cc1
FormulaC28 H25 Cl F2 N2 O3
Name4-{(2S)-2-[2-(4-chlorophenyl)-5,6-difluoro-1H-benzimidazol-1-yl]-2-cyclohexylethoxy}benzoic acid
ChEMBL
DrugBank
ZINC
PDB chain5q0p 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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PDB5q0p D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		I273 I277 M294 M332 F333 R335 S336 I339 F340 I356 S359 M369 Y373
Binding residue
(residue number reindexed from 1)		I27 I31 M48 M86 F87 R89 S90 I93 F94 I110 S113 M123 Y127
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.41,IC50=0.039uM
BindingDB: IC50=39nM
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:5q0p, PDBe:5q0p, PDBj:5q0p
PDBsum5q0p
PubMed29204945
UniProtQ96RI1|NR1H4_HUMAN Bile acid receptor (Gene Name=NR1H4)

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