Structure of PDB 3kdu Chain A Binding Site BS01

Receptor Information
>3kdu Chain A (length=264) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SETADLKSLAKRIYEAYLKNFNMNKVKARVILSGKASNNPPFVIHDMETL
CMAEKTLVAIQNKEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLN
DQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITREFLKSLRKPFCD
IMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQEG
IVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLVQIIKKTESD
AALHPLLQEIYRDM
Ligand information
Ligand IDNKS
InChIInChI=1S/C28H25ClN2O6/c1-18-6-12-23(13-7-18)37-28(34)31(16-26(32)33)15-20-4-3-5-24(14-20)35-17-25-19(2)36-27(30-25)21-8-10-22(29)11-9-21/h3-14H,15-17H2,1-2H3,(H,32,33)
InChIKeyHUZRXZVIBUNCKL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.352Cc1ccc(OC(=O)N(CC(O)=O)Cc2cccc(OCc3nc(oc3C)c4ccc(Cl)cc4)c2)cc1
ACDLabs 11.02O=C(Oc1ccc(cc1)C)N(CC(=O)O)Cc4cc(OCc2nc(oc2C)c3ccc(Cl)cc3)ccc4
OpenEye OEToolkits 1.7.0Cc1ccc(cc1)OC(=O)N(Cc2cccc(c2)OCc3c(oc(n3)c4ccc(cc4)Cl)C)CC(=O)O
FormulaC28 H25 Cl N2 O6
NameN-(3-{[2-(4-chlorophenyl)-5-methyl-1,3-oxazol-4-yl]methoxy}benzyl)-N-[(4-methylphenoxy)carbonyl]glycine
ChEMBLCHEMBL1089210
DrugBank
ZINCZINC000044460340
PDB chain3kdu Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3kdu Discovery of an oxybenzylglycine based peroxisome proliferator activated receptor alpha selective agonist 2-((3-((2-(4-chlorophenyl)-5-methyloxazol-4-yl)methoxy)benzyl)(methoxycarbonyl)amino)acetic acid (BMS-687453).
Resolution2.07 Å
Binding residue
(original residue number in PDB)		F273 C276 S280 Y314 L321 M330 V332 I354 M355 H440
Binding residue
(residue number reindexed from 1)		F70 C73 S77 Y111 L118 M127 V129 I151 M152 H237
Annotation score1
Binding affinityMOAD: ic50=347nM
PDBbind-CN: -logKd/Ki=6.46,IC50=347nM
BindingDB: IC50=347nM,EC50=8nM
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:3kdu, PDBe:3kdu, PDBj:3kdu
PDBsum3kdu
PubMed20218621
UniProtQ07869|PPARA_HUMAN Peroxisome proliferator-activated receptor alpha (Gene Name=PPARA)

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