Structure of PDB 6c5q Chain A Binding Site BS01

Receptor Information
>6c5q Chain A (length=278) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHHGSHMESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVI
YDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEY
AKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMT
REFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPG
LLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEH
VQLLQVIKKTETDMSLHPLLQEIYKDLY
Ligand information
Ligand IDEKS
InChIInChI=1S/C34H40N2O4/c1-21-23(3)36(20-24-10-9-11-28(18-24)40-34(7,8)32(38)39)30-17-14-26(19-29(21)30)31(37)35-22(2)25-12-15-27(16-13-25)33(4,5)6/h9-19,22H,20H2,1-8H3,(H,35,37)(H,38,39)/t22-/m0/s1
InChIKeyDLXSTRGKTJFVEB-QFIPXVFZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1c(n(c2c1cc(cc2)C(=O)N[C@@H](C)c3ccc(cc3)C(C)(C)C)Cc4cccc(c4)OC(C)(C)C(=O)O)C
ACDLabs 12.01Cc3c2c(ccc(C(=O)NC(c1ccc(cc1)C(C)(C)C)C)c2)n(c3C)Cc4cccc(c4)OC(C(O)=O)(C)C
OpenEye OEToolkits 2.0.6Cc1c(n(c2c1cc(cc2)C(=O)NC(C)c3ccc(cc3)C(C)(C)C)Cc4cccc(c4)OC(C)(C)C(=O)O)C
CACTVS 3.385C[C@H](NC(=O)c1ccc2n(Cc3cccc(OC(C)(C)C(O)=O)c3)c(C)c(C)c2c1)c4ccc(cc4)C(C)(C)C
CACTVS 3.385C[CH](NC(=O)c1ccc2n(Cc3cccc(OC(C)(C)C(O)=O)c3)c(C)c(C)c2c1)c4ccc(cc4)C(C)(C)C
FormulaC34 H40 N2 O4
Name2-{3-[(5-{[(1S)-1-(4-tert-butylphenyl)ethyl]carbamoyl}-2,3-dimethyl-1H-indol-1-yl)methyl]phenoxy}-2-methylpropanoic acid
ChEMBLCHEMBL3678120
DrugBank
ZINCZINC000206000535
PDB chain6c5q 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6c5q PPAR gamma in Complex with an Antagonist and Inverse Agonist: a Tumble and Trap Mechanism of the Activation Helix.
Resolution2.404 Å
Binding residue
(original residue number in PDB)		G284 C285 F287 R288 M329 L330 L333 I341 S342 Y473
Binding residue
(residue number reindexed from 1)		G85 C86 F88 R89 M130 L131 L134 I142 S143 Y274
Annotation score1
Binding affinityMOAD: ic50=220nM
PDBbind-CN: -logKd/Ki=6.66,IC50=220nM
BindingDB: IC50=321nM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6c5q, PDBe:6c5q, PDBj:6c5q
PDBsum6c5q
PubMed30123887
UniProtP37231|PPARG_HUMAN Peroxisome proliferator-activated receptor gamma (Gene Name=PPARG)

[Back to BioLiP]