Structure of PDB 3i28 Chain A Binding Site BS01

Receptor Information

>3i28 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 ID

34N

InChI

InChI=1S/C24H21FN2O3S/c1-31(29,30)22-12-8-19(9-13-22)23(18-6-10-21(25)11-7-18)14-15-27-24(28)20-4-2-17(16-26)3-5-20/h2-13,23H,14-15H2,1H3,(H,27,28)/t23-/m0/s1

InChIKey

OXJGQTIVCHEXQS-QHCPKHFHSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.0	CS(=O)(=O)c1ccc(cc1)[C@@H](CCNC(=O)c2ccc(cc2)C#N)c3ccc(cc3)F
CACTVS 3.370	C[S](=O)(=O)c1ccc(cc1)[CH](CCNC(=O)c2ccc(cc2)C#N)c3ccc(F)cc3
OpenEye OEToolkits 1.7.0	CS(=O)(=O)c1ccc(cc1)C(CCNC(=O)c2ccc(cc2)C#N)c3ccc(cc3)F
CACTVS 3.370	C[S](=O)(=O)c1ccc(cc1)[C@@H](CCNC(=O)c2ccc(cc2)C#N)c3ccc(F)cc3
ACDLabs 12.01	O=S(=O)(c1ccc(cc1)C(c2ccc(F)cc2)CCNC(=O)c3ccc(C#N)cc3)C

Formula

C24 H21 F N2 O3 S

Name

4-cyano-N-{(3S)-3-(4-fluorophenyl)-3-[4-(methylsulfonyl)phenyl]propyl}benzamide

PDB chain

3i28 Chain A Residue 999 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	3i28 Structure-based optimization of arylamides as inhibitors of soluble epoxide hydrolase.
Resolution	1.95 Å
Binding residue (original residue number in PDB)	F267 D335 W336 M339 Y383 L408 M419 Y466 F497 V498 H524
Binding residue (residue number reindexed from 1)	F264 D332 W333 M336 Y380 L405 M416 Y463 F494 V495 H521
Annotation score	1
Binding affinity	MOAD: ic50=6nM PDBbind-CN: -logKd/Ki=8.22,IC50=6nM BindingDB: IC50=8nM,EC50=0.14nM

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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External links

PDB	RCSB:3i28, PDBe:3i28, PDBj:3i28
PDBsum	3i28
PubMed	19746975
UniProt	P34913\|HYES_HUMAN Bifunctional epoxide hydrolase 2 (Gene Name=EPHX2)

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