Structure of PDB 1zd2 Chain P Binding Site BS02

Receptor Information
>1zd2 Chain P (length=547) 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
QMSQHMEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDARN
Ligand information
Ligand IDNC3
InChIInChI=1S/C9H16N2O3/c12-8(13)6-10-9(14)11-7-4-2-1-3-5-7/h7H,1-6H2,(H,12,13)(H2,10,11,14)
InChIKeyNVORCMBCUHQRDL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC(=O)CNC(=O)NC1CCCCC1
ACDLabs 10.04O=C(NC1CCCCC1)NCC(=O)O
OpenEye OEToolkits 1.5.0C1CCC(CC1)NC(=O)NCC(=O)O
FormulaC9 H16 N2 O3
NameN-[(CYCLOHEXYLAMINO)CARBONYL]GLYCINE;
4-(3-CYCLOHEXYLURIEDO)-ETHANOIC ACID
ChEMBLCHEMBL66380
DrugBankDB08256
ZINCZINC000006691828
PDB chain1zd2 Chain P Residue 700 [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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PDB1zd2 Human soluble epoxide hydrolase: structural basis of inhibition by 4-(3-cyclohexylureido)-carboxylic acids
Resolution3.0 Å
Binding residue
(original residue number in PDB)		F265 D333 W334 Y381 M418 Y465 H523 W524
Binding residue
(residue number reindexed from 1)		F266 D334 W335 Y382 M418 Y465 H523 W524
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.30,IC50>500uM
BindingDB: IC50=>500000nM
Enzymatic activity
Catalytic site (original residue number in PDB) F265 W334 N376 Y381 D495 H523
Catalytic site (residue number reindexed from 1) F266 W335 N377 Y382 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:1zd2, PDBe:1zd2, PDBj:1zd2
PDBsum1zd2
PubMed16322563
UniProtP34913|HYES_HUMAN Bifunctional epoxide hydrolase 2 (Gene Name=EPHX2)

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