Structure of PDB 1zd3 Chain A Binding Site BS02

Receptor Information
>1zd3 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]
TLRAAVFDLDGVLALPAVFGVLGRTEEALALPRGLLNDAFQKGGPEGATT
RLMKGEITLSQWIPLMEENCRKCSETAKVCLPKNFSIKEIFDKAISARKI
NRPMLQAALMLRKKGFTTAILTNTWLDDRAERDGLAQLMCELKMHFDFLI
ESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTI
LVQDTDTALKELEKVTGIQLLNTPAPLPTSCNPSDMSHGYVTVKPRVRLH
FVELGSGPAVCLCHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESSA
PPEIEEYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPER
VRAVASLNTPFIPANPNMSPLESIKANPVFDYQLYFQEPGVAEAELEQNL
SRTFKSLFRASDESVLSMHKVCEAGGLFVNSPEEPSLSRMVTEEEIQFYV
QQFKKSGFRGPLNWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLVP
QMSQHMEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDARN
Ligand information
Ligand IDNC4
InChIInChI=1S/C11H20N2O3/c14-10(15)7-4-8-12-11(16)13-9-5-2-1-3-6-9/h9H,1-8H2,(H,14,15)(H2,12,13,16)
InChIKeyWSVFRGGLURJIMG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1CCC(CC1)NC(=O)NCCCC(=O)O
ACDLabs 10.04O=C(NC1CCCCC1)NCCCC(=O)O
CACTVS 3.341OC(=O)CCCNC(=O)NC1CCCCC1
FormulaC11 H20 N2 O3
Name4-{[(CYCLOHEXYLAMINO)CARBONYL]AMINO}BUTANOIC ACID;
4-(3-CYCLOHEXYLURIEDO)-BUTYRIC ACID
ChEMBLCHEMBL219695
DrugBankDB08257
ZINCZINC000008754389
PDB chain1zd3 Chain A Residue 790 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1zd3 Human soluble epoxide hydrolase: structural basis of inhibition by 4-(3-cyclohexylureido)-carboxylic acids
Resolution2.3 Å
Binding residue
(original residue number in PDB)		D333 W334 Y381 Q382 M418 Y465 H523 W524
Binding residue
(residue number reindexed from 1)		D334 W335 Y382 Q383 M418 Y465 H523 W524
Annotation score1
Binding affinityMOAD: ic50>500uM
PDBbind-CN: -logKd/Ki=3.30,IC50>500uM
BindingDB: IC50=36000nM
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) 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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1zd3, PDBe:1zd3, PDBj:1zd3
PDBsum1zd3
PubMed16322563
UniProtP34913|HYES_HUMAN Bifunctional epoxide hydrolase 2 (Gene Name=EPHX2)

[Back to BioLiP]