Structure of PDB 3s9s Chain A Binding Site BS02

Receptor Information
>3s9s Chain A (length=258) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SADLRALAKHLYDSYIKSFPLTKAKARAILTGKSPFVIYDMNSLMMGEDK
IKFKHITKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTL
LKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPK
FEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQAL
ELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETMSLHPL
LQEIYKDL
Ligand information
Ligand IDM0T
InChIInChI=1S/C25H23Cl2N3O/c1-3-22(18-7-5-4-6-8-18)29-25(31)19-10-12-24-23(14-19)28-16(2)30(24)15-17-9-11-20(26)21(27)13-17/h4-14,22H,3,15H2,1-2H3,(H,29,31)/t22-/m1/s1
InChIKeyLDYDIGPGIRJQAU-JOCHJYFZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CCC(c1ccccc1)NC(=O)c2ccc3c(c2)nc(n3Cc4ccc(c(c4)Cl)Cl)C
OpenEye OEToolkits 1.7.0CC[C@H](c1ccccc1)NC(=O)c2ccc3c(c2)nc(n3Cc4ccc(c(c4)Cl)Cl)C
CACTVS 3.370CC[C@@H](NC(=O)c1ccc2n(Cc3ccc(Cl)c(Cl)c3)c(C)nc2c1)c4ccccc4
ACDLabs 12.01Clc1ccc(cc1Cl)Cn2c3ccc(cc3nc2C)C(=O)NC(c4ccccc4)CC
CACTVS 3.370CC[CH](NC(=O)c1ccc2n(Cc3ccc(Cl)c(Cl)c3)c(C)nc2c1)c4ccccc4
FormulaC25 H23 Cl2 N3 O
Name1-(3,4-dichlorobenzyl)-2-methyl-N-[(1R)-1-phenylpropyl]-1H-benzimidazole-5-carboxamide
ChEMBLCHEMBL1825106
DrugBank
ZINCZINC000072182088
PDB chain3s9s 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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PDB3s9s Discovery of GSK1997132B a novel centrally penetrant benzimidazole PPARgamma partial agonist.
Resolution2.55 Å
Binding residue
(original residue number in PDB)		F282 C285 Q286 R288 S289 H323 Y327 L330 I341 F363 M364 H449 Y473
Binding residue
(residue number reindexed from 1)		F65 C68 Q69 R71 S72 H106 Y110 L113 I124 F146 M147 H232 Y255
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0004879 nuclear receptor activity
Biological Process
GO:0006355 regulation of DNA-templated transcription
Cellular Component
GO:0005634 nucleus

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3s9s, PDBe:3s9s, PDBj:3s9s
PDBsum3s9s
PubMed21798739
UniProtP37231|PPARG_HUMAN Peroxisome proliferator-activated receptor gamma (Gene Name=PPARG)

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