Structure of PDB 3i1y Chain A Binding Site BS01

Receptor Information
>3i1y Chain A (length=545) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RAAVFDLDGVLALPAVFGVLGRTEEALALPRGLLNDAFQKGGPEGATTRL
MKGEITLSQWIPLMEENCRKCSETAKVCLPKNFSIKEIFDKAISARKINR
PMLQAALMLRKKGFTTAILTNTWLDDRAERDGLAQLMCELKMHFDFLIES
CQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILV
QDTDTALKELEKVTGIQLLNTPAPLPTSCNPSDMSHGYVTVKPRVRLHFV
ELGSGPAVCLCHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESSAPP
EIEEYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPERVR
AVASLNTPFIPANPNMSPLESIKANPVFDYQLYFQEPGVAEAELEQNLSR
TFKSLFRASDESVLSMHKVCEAGGLFVNSPEEPSLSRMVTEEEIQFYVQQ
FKKSGFRGPLNWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLVPQM
SQHMEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDARN
Ligand information
Ligand ID33N
InChIInChI=1S/C21H20N2O/c24-21(19-12-7-14-22-16-19)23-15-13-20(17-8-3-1-4-9-17)18-10-5-2-6-11-18/h1-12,14,16,20H,13,15H2,(H,23,24)
InChIKeyGDHXZIQAOUBZCC-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1ccc(cc1)C(CCNC(=O)c2cccnc2)c3ccccc3
ACDLabs 10.04
CACTVS 3.341		O=C(NCCC(c1ccccc1)c2ccccc2)c3cccnc3
FormulaC21 H20 N2 O
NameN-(3,3-diphenylpropyl)pyridine-3-carboxamide;
N-(3,3-Diphenyl-propyl)-nicotinamide
ChEMBLCHEMBL560537
DrugBank
ZINCZINC000004401896
PDB chain3i1y Chain A Residue 999 [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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PDB3i1y Structure-based optimization of arylamides as inhibitors of soluble epoxide hydrolase.
Resolution2.469 Å
Binding residue
(original residue number in PDB)		D335 W336 Y383 Q384 L408 M419 Y466 V498 H524 W525
Binding residue
(residue number reindexed from 1)		D332 W333 Y380 Q381 L405 M416 Y463 V495 H521 W522
Annotation score1
Binding affinityMOAD: ic50=7nM
PDBbind-CN: -logKd/Ki=8.15,IC50=7nM
BindingDB: IC50=7nM
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.
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:3i1y, PDBe:3i1y, PDBj:3i1y
PDBsum3i1y
PubMed19746975
UniProtP34913|HYES_HUMAN Bifunctional epoxide hydrolase 2 (Gene Name=EPHX2)

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