Structure of PDB 4y2p Chain A Binding Site BS02

Receptor Information
>4y2p Chain A (length=546) 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
QMSQHMEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDAR
Ligand information
Ligand ID3C5
InChIInChI=1S/C13H14N2/c1-14-9-11-4-2-5-12(8-11)13-6-3-7-15-10-13/h2-8,10,14H,9H2,1H3
InChIKeyLZJRRTLTBULOHU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385
OpenEye OEToolkits 1.9.2		CNCc1cccc(c1)c2cccnc2
ACDLabs 12.01n2cccc(c1cc(ccc1)CNC)c2
FormulaC13 H14 N2
NameN-methyl-1-[3-(pyridin-3-yl)phenyl]methanamine
ChEMBLCHEMBL3402235
DrugBank
ZINCZINC000003880944
PDB chain4y2p Chain A Residue 602 [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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PDB4y2p Identification of N-ethylmethylamine as a novel scaffold for inhibitors of soluble epoxide hydrolase by crystallographic fragment screening
Resolution2.05 Å
Binding residue
(original residue number in PDB)		F267 D335 Y383 Y466 H524 W525
Binding residue
(residue number reindexed from 1)		F266 D334 Y382 Y465 H523 W524
Annotation score1
Binding affinityMOAD: ic50=2200uM
PDBbind-CN: -logKd/Ki=2.66,IC50=2200uM
BindingDB: IC50=2200000nM
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) 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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4y2p, PDBe:4y2p, PDBj:4y2p
PDBsum4y2p
PubMed25862210
UniProtP34913|HYES_HUMAN Bifunctional epoxide hydrolase 2 (Gene Name=EPHX2)

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