Structure of PDB 4od0 Chain A Binding Site BS02

Receptor Information
>4od0 Chain A (length=547) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTLRAAVFDLDGVLALPAVFGVLGRTEEALALPRGLLNDAFQKGGPEGAT
TRLMKGEITLSQWIPLMEENCRKCSETAKVCLPKNFSIKEIFDKAISARK
INRPMLQAALMLRKKGFTTAILTNTWLDDRAERDGLAQLMCELKMHFDFL
IESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVT
ILVQDTDTALKELEKVTGIQLLNTPAPLPTSCNPSDMSHGYVTVKPRVRL
HFVELGSGPAVCLCHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESS
APPEIEEYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPE
RVRAVASLNTPFIPANPNMSPLESIKANPVFDYQLYFQEPGVAEAELEQN
LSRTFKSLFRASDESVLSMHKVCEAGGLFVNSPEEPSLSRMVTEEEIQFY
VQQFKKSGFRGPLNWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLV
PQMSQHMEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDAR
Ligand information
Ligand ID2RV
InChIInChI=1S/C16H20F3N3O3/c1-2-14(23)22-9-7-12(8-10-22)21-15(24)20-11-3-5-13(6-4-11)25-16(17,18)19/h3-6,12H,2,7-10H2,1H3,(H2,20,21,24)
InChIKeyAAJMQTLFRTZCJK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(N2CCC(NC(=O)Nc1ccc(OC(F)(F)F)cc1)CC2)CC
OpenEye OEToolkits 1.7.6CCC(=O)N1CCC(CC1)NC(=O)Nc2ccc(cc2)OC(F)(F)F
CACTVS 3.385CCC(=O)N1CCC(CC1)NC(=O)Nc2ccc(OC(F)(F)F)cc2
FormulaC16 H20 F3 N3 O3
Name1-(1-propanoylpiperidin-4-yl)-3-[4-(trifluoromethoxy)phenyl]urea
ChEMBLCHEMBL1258904
DrugBank
ZINCZINC000036388980
PDB chain4od0 Chain A Residue 603 [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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PDB4od0 Optimized inhibitors of soluble epoxide hydrolase improve in vitro target residence time and in vivo efficacy.
Resolution2.92 Å
Binding residue
(original residue number in PDB)		F267 D335 W336 Y383 L408 M419 L428 Y466
Binding residue
(residue number reindexed from 1)		F267 D335 W336 Y383 L408 M419 L428 Y466
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.04,Ki=0.91nM
BindingDB: IC50=3.7nM,Ki=0.910nM
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) F267 H334 D335 W336 N359 N378 Y383 Y466 D496 H524
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:4od0, PDBe:4od0, PDBj:4od0
PDBsum4od0
PubMed25079952
UniProtP34913|HYES_HUMAN Bifunctional epoxide hydrolase 2 (Gene Name=EPHX2)

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