Structure of PDB 3koo Chain A Binding Site BS01

Receptor Information
>3koo Chain A (length=545) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RAAVFDLDGVLALPAVFGVLGRTEEALALPRGLLNDAFQKGGPEGATTRL
MKGEITLSQWIPLMEENCRKCSETAKVCLPKNFSIKEIFDKAISARKINR
PMLQAALMLRKKGFTTAILTNTWLDDRAERDGLAQLMCELKMHFDFLIES
CQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILV
QDTDTALKELEKVTGIQLLNTPAPLPTSCNPSDMSHGYVTVKPRVRLHFV
ELGSGPAVCLCHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESSAPP
EIEEYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPERVR
AVASLNTPFIPANPNMSPLESIKANPVFDYQLYFQEPGVAEAELEQNLSR
TFKSLFRASDESVLSMHKVCEAGGLFVNSPEEPSLSRMVTEEEIQFYVQQ
FKKSGFRGPLNWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLVPQM
SQHMEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDARN
Ligand information
Ligand ID24D
InChIInChI=1S/C17H18Cl2N4O2/c18-13-3-2-12(15(19)10-13)11-22-17(24)23-8-4-14(5-9-23)25-16-20-6-1-7-21-16/h1-3,6-7,10,14H,4-5,8-9,11H2,(H,22,24)
InChIKeyUZEPPAOAIDTLTK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.352Clc1ccc(CNC(=O)N2CCC(CC2)Oc3ncccn3)c(Cl)c1
OpenEye OEToolkits 1.7.0c1cnc(nc1)OC2CCN(CC2)C(=O)NCc3ccc(cc3Cl)Cl
FormulaC17 H18 Cl2 N4 O2
NameN-(2,4-dichlorobenzyl)-4-(pyrimidin-2-yloxy)piperidine-1-carboxamide;
4-(Pyrimidin-2-yloxy)-piperidine-1-carboxylic acid 2,4-dichloro-benzylamide
ChEMBLCHEMBL589136
DrugBank
ZINCZINC000044460348
PDB chain3koo Chain A Residue 556 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3koo Optimization of piperidyl-ureas as inhibitors of soluble epoxide hydrolase.
Resolution2.791 Å
Binding residue
(original residue number in PDB)
F267 D335 W336 M339 Y383 Q384 Y466 F497 V498 L499 M503 H524
Binding residue
(residue number reindexed from 1)
F264 D332 W333 M336 Y380 Q381 Y463 F494 V495 L496 M500 H521
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.82,IC50=15nM
BindingDB: IC50=15nM
Enzymatic activity
Catalytic site (original residue number in PDB) F267 H334 D335 W336 N359 N378 Y383 Y466 D496 H524
Catalytic site (residue number reindexed from 1) F264 H331 D332 W333 N356 N375 Y380 Y463 D493 H521
Enzyme Commision number 3.1.3.76: lipid-phosphate phosphatase.
3.3.2.10: soluble epoxide hydrolase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0004301 epoxide hydrolase activity
GO:0015643 toxic substance binding
GO:0016787 hydrolase activity
GO:0016791 phosphatase activity
GO:0033885 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity
GO:0042577 lipid phosphatase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0052642 lysophosphatidic acid phosphatase activity
Biological Process
GO:0006629 lipid metabolic process
GO:0009056 catabolic process
GO:0009636 response to toxic substance
GO:0010628 positive regulation of gene expression
GO:0016311 dephosphorylation
GO:0042632 cholesterol homeostasis
GO:0046272 stilbene catabolic process
GO:0046839 phospholipid dephosphorylation
GO:0090181 regulation of cholesterol metabolic process
GO:0097176 epoxide metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005777 peroxisome
GO:0005782 peroxisomal matrix
GO:0005829 cytosol
GO:0070062 extracellular exosome

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:3koo, PDBe:3koo, PDBj:3koo
PDBsum3koo
PubMed19969453
UniProtP34913|HYES_HUMAN Bifunctional epoxide hydrolase 2 (Gene Name=EPHX2)

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