Structure of PDB 3koo Chain A

Receptor sequence
>3kooA (length=545) Species: 9606 (Homo sapiens) [Search protein sequence]
RAAVFDLDGVLALPAVFGVLGRTEEALALPRGLLNDAFQKGGPEGATTRL
MKGEITLSQWIPLMEENCRKCSETAKVCLPKNFSIKEIFDKAISARKINR
PMLQAALMLRKKGFTTAILTNTWLDDRAERDGLAQLMCELKMHFDFLIES
CQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILV
QDTDTALKELEKVTGIQLLNTPAPLPTSCNPSDMSHGYVTVKPRVRLHFV
ELGSGPAVCLCHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESSAPP
EIEEYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPERVR
AVASLNTPFIPANPNMSPLESIKANPVFDYQLYFQEPGVAEAELEQNLSR
TFKSLFRASDESVLSMHKVCEAGGLFVNSPEEPSLSRMVTEEEIQFYVQQ
FKKSGFRGPLNWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLVPQM
SQHMEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDARN
3D structure
PDB3koo Optimization of piperidyl-ureas as inhibitors of soluble epoxide hydrolase.
ChainA
Resolution2.791 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
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.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 24D A F267 D335 W336 M339 Y383 Q384 Y466 F497 V498 L499 M503 H524 F264 D332 W333 M336 Y380 Q381 Y463 F494 V495 L496 M500 H521 PDBbind-CN: -logKd/Ki=7.82,IC50=15nM
BindingDB: IC50=15nM
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:3koo, PDBe:3koo, PDBj:3koo
PDBsum3koo
PubMed19969453
UniProtP34913|HYES_HUMAN Bifunctional epoxide hydrolase 2 (Gene Name=EPHX2)

[Back to BioLiP]