Structure of PDB 3pdc Chain A Binding Site BS01

Receptor Information
>3pdc Chain A (length=323) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APLPTSCNPSDMSHGYVTVKPRVRLHFVELGSGPAVCLCHGFPESWYSWR
YQIPALAQAGYRVLAMDMKGYGESSAPPEIEEYCMEVLCKEMVTFLDKLG
LSQAVFIGHDWGGMLVWYMALFYPERVRAVASLNTPFIPANPNMSPLESI
KANPVFDYQLYFQEPGVAEAELEQNLSRTFKSLFRASDESVLSMHKVCEA
GGLFVNSPEEPSLSRMVTEEEIQFYVQQFKKSGFRGPLNWYRNMERNWKW
ACKSLGRKILIPALMVTAEKDFVLVPQMSQHMEDWIPHLKRGHIEDCGHW
TQMDKPTEVNQILIKWLDSDARN
Ligand information
Ligand IDZYI
InChIInChI=1S/C14H15ClN2O2/c15-10-5-6-12-11(8-10)16-14(19-12)17-13(18)7-9-3-1-2-4-9/h5-6,8-9H,1-4,7H2,(H,16,17,18)
InChIKeyQXFNONNLQZPIAQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Clc1ccc2oc(NC(=O)CC3CCCC3)nc2c1
OpenEye OEToolkits 1.7.0c1cc2c(cc1Cl)nc(o2)NC(=O)CC3CCCC3
ACDLabs 12.01Clc1cc2nc(oc2cc1)NC(=O)CC3CCCC3
FormulaC14 H15 Cl N2 O2
NameN-(5-chloro-1,3-benzoxazol-2-yl)-2-cyclopentylacetamide
ChEMBLCHEMBL1689794
DrugBank
ZINC
PDB chain3pdc 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

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PDB3pdc Discovery of potent inhibitors of soluble epoxide hydrolase by combinatorial library design and structure-based virtual screening.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		F265 D333 M337 T358 Y381 Y465 H523 W524
Binding residue
(residue number reindexed from 1)		F42 D110 M114 T135 Y158 Y241 H299 W300
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.49,IC50=32nM
Enzymatic activity
Catalytic site (original residue number in PDB) F265 H332 D333 W334 N357 N376 Y381 Y465 D495 H523
Catalytic site (residue number reindexed from 1) F42 H109 D110 W111 N134 N153 Y158 Y241 D271 H299
Enzyme Commision number 3.1.3.76: lipid-phosphate phosphatase.
3.3.2.10: soluble epoxide hydrolase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity

View graph for
Molecular Function
External links
PDB RCSB:3pdc, PDBe:3pdc, PDBj:3pdc
PDBsum3pdc
PubMed21302953
UniProtP34913|HYES_HUMAN Bifunctional epoxide hydrolase 2 (Gene Name=EPHX2)

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