Structure of PDB 3gz9 Chain A Binding Site BS02

Receptor Information
>3gz9 Chain A (length=262) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QVADLKAFSKHIYNAYLKNFNMTKKKARSILTGKAAPFVIHDIETLWQAE
KGLVWKGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFGSLFLND
QVTLLKYGVHEAIFAMLASLVNKDGLLVANGSGFVTREFLRSLRKPFSDI
IEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTI
LRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETET
SLHPLLQEIYKD
Ligand information
Ligand IDD32
InChIInChI=1S/C27H23F3O5S/c1-4-13-33-23-14-19(15-34-21-8-6-20(7-9-21)27(28,29)30)5-11-25(23)36-24-12-10-22(17(2)18(24)3)35-16-26(31)32/h1,5-12,14H,13,15-16H2,2-3H3,(H,31,32)
InChIKeyRMMWVBYHCKSFMW-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(c(ccc1OCC(=O)O)Sc2ccc(cc2OCC#C)COc3ccc(cc3)C(F)(F)F)C
CACTVS 3.341Cc1c(C)c(Sc2ccc(COc3ccc(cc3)C(F)(F)F)cc2OCC#C)ccc1OCC(O)=O
ACDLabs 10.04FC(F)(F)c3ccc(OCc2ccc(Sc1c(c(c(OCC(=O)O)cc1)C)C)c(OCC#C)c2)cc3
FormulaC27 H23 F3 O5 S
Name(2,3-dimethyl-4-{[2-(prop-2-yn-1-yloxy)-4-{[4-(trifluoromethyl)phenoxy]methyl}phenyl]sulfanyl}phenoxy)acetic acid
ChEMBLCHEMBL524063
DrugBank
ZINCZINC000038139028
PDB chain3gz9 Chain A Residue 1 [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]
PDB3gz9 Identification of a PPARdelta agonist with partial agonistic activity on PPARgamma.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		F282 R284 C285 T289 H323 L330 L339 V341 V348 I364 K367 H449 M453 L469 Y473
Binding residue
(residue number reindexed from 1)		F69 R71 C72 T76 H110 L117 L126 V128 V135 I151 K154 H236 M240 L256 Y260
Annotation score1
Binding affinityMOAD: Ki=0.004uM
PDBbind-CN: -logKd/Ki=8.40,IC50=4nM
BindingDB: EC50=54nM,Ki=4nM
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:3gz9, PDBe:3gz9, PDBj:3gz9
PDBsum3gz9
PubMed19464171
UniProtQ03181|PPARD_HUMAN Peroxisome proliferator-activated receptor delta (Gene Name=PPARD)

[Back to BioLiP]