Structure of PDB 5ak6 Chain A Binding Site BS02

Receptor Information

>5ak6 Chain A (length=541) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

TLRAAVFDLDGVLALPAVFGVLGRTEEALALPRGLLNDAFQKGGPEGATT
RLMKGEITLSQWIPLMEENCRKCSCLPKNFSIKEIFDKAISARKINRPML
QAALMLRKKGFTTAILTNTWLDDRAERDGLAQLMCELKMHFDFLIESCQV
GMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILVQDT
DTALKELEKVTGIQLLNTPAPLPTSCNPSDMSHGYVTVKPRVRLHFVELG
SGPAVCLCHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESSAPPEIE
EYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPERVRAVA
SLNTPFIPANPNMSPLESIKANPVFDYQLYFQEPGVAEAELEQNLSRTFK
SLFRASDESVLSMHKVCEAGGLFVNSPEEPSLSRMVTEEEIQFYVQQFKK
SGFRGPLNWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLVPQMSQH
MEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDAR

Ligand information

Ligand ID

YPN

InChI

InChI=1S/C7H8ClNOS/c8-6-1-2-7(9-5-6)11-4-3-10/h1-2,5,10H,3-4H2

InChIKey

KLOJLJIHCJJDCT-UHFFFAOYSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.6	c1cc(ncc1Cl)SCCO
CACTVS 3.385	OCCSc1ccc(Cl)cn1

Formula

C7 H8 Cl N O S

Name

2-[(5-CHLORO-2-PYRIDYL)SULFANYL]ETHANOL

PDB chain

5ak6 Chain A Residue 1554 [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	5ak6 Successful Generation of Structural Information for Fragment-Based Drug Discovery.
Resolution	2.15 Å
Binding residue (original residue number in PDB)	M419 V498 H524 W525
Binding residue (residue number reindexed from 1)	M413 V492 H518 W519
Annotation score	1
Binding affinity	MOAD: ic50=326.4uM PDBbind-CN: -logKd/Ki=3.49,IC50=326.4uM

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)	F261 H328 D329 W330 N353 N372 Y377 Y460 D490 H518
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:5ak6, PDBe:5ak6, PDBj:5ak6
PDBsum	5ak6
PubMed	25931264
UniProt	P34913\|HYES_HUMAN Bifunctional epoxide hydrolase 2 (Gene Name=EPHX2)

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