Structure of PDB 3wk7 Chain A Binding Site BS02

Receptor Information
>3wk7 Chain A (length=546) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TLRAAVFDLDGVLALPAVFGVLGRTEEALALPRGLLNDAFQKGGPEGATT
RLMKGEITLSQWIPLMEENCRKCSETAKVCLPKNFSIKEIFDKAISARKI
NRPMLQAALMLRKKGFTTAILTNTWLDDRAERDGLAQLMCELKMHFDFLI
ESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTI
LVQDTDTALKELEKVTGIQLLNTPAPLPTSCNPSDMSHGYVTVKPRVRLH
FVELGSGPAVCLCHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESSA
PPEIEEYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPER
VRAVASLNTPFIPANPNMSPLESIKANPVFDYQLYFQEPGVAEAELEQNL
SRTFKSLFRASDESVLSMHKVCEAGGLFVNSPEEPSLSRMVTEEEIQFYV
QQFKKSGFRGPLNWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLVP
QMSQHMEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDAR
Ligand information
Ligand IDS0D
InChIInChI=1S/C11H10N4/c1-15-7-8(6-12-15)11-13-9-4-2-3-5-10(9)14-11/h2-7H,1H3,(H,13,14)
InChIKeyILAJBGJRKOVOJZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01n3cc(c1nc2c(n1)cccc2)cn3C
CACTVS 3.385
OpenEye OEToolkits 1.7.6		Cn1cc(cn1)c2[nH]c3ccccc3n2
FormulaC11 H10 N4
Name2-(1-methyl-1H-pyrazol-4-yl)-1H-benzimidazole
ChEMBLCHEMBL3233605
DrugBank
ZINCZINC000009337925
PDB chain3wk7 Chain A Residue 603 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3wk7 Structural insights into binding of inhibitors to soluble epoxide hydrolase gained by fragment screening and X-ray crystallography.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		D335 W336 Y383 Y466 W525
Binding residue
(residue number reindexed from 1)		D334 W335 Y382 Y465 W524
Annotation score1
Binding affinityMOAD: ic50=127uM
PDBbind-CN: -logKd/Ki=3.90,IC50=127uM
BindingDB: IC50=127000nM
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) F266 H333 D334 W335 N358 N377 Y382 Y465 D495 H523
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:3wk7, PDBe:3wk7, PDBj:3wk7
PDBsum3wk7
PubMed24656800
UniProtP34913|HYES_HUMAN Bifunctional epoxide hydrolase 2 (Gene Name=EPHX2)

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