Structure of PDB 5akk Chain A Binding Site BS02

Receptor Information
>5akk 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
RLMKGEITLSQWIPLMEENCRKCSETAKVCNFSIKEIFDKAISARKINRP
MLQAALMLRKKGFTTAILTNTWLDDRAERDGLAQLMCELKMHFDFLIESC
QVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILVQ
DTDTALKELEKVTGIQLLNTPAPLPTSCNPSDMSHGYVTVKPRVRLHFVE
LGSGPAVCLCHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESSAPPE
IEEYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPERVRA
VASLNTPFIPANPNMSPLESIKANPVFDYQLYFQEPGVAEAELEQNLSRT
FKSLFRASDESVLSMHKVAGGLFVNSPEEPSLSRMVTEEEIQFYVQQFKK
SGFRGPLNWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLVPQMSQH
MEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDAR
Ligand information
Ligand ID1P8
InChIInChI=1S/C8H6BrNO/c9-6-2-1-5-3-8(11)10-7(5)4-6/h1-2,4H,3H2,(H,10,11)
InChIKeyJARRYVQFBQVOBE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01Brc1ccc2c(c1)NC(=O)C2
OpenEye OEToolkits 1.7.6c1cc2c(cc1Br)NC(=O)C2
CACTVS 3.370Brc1ccc2CC(=O)Nc2c1
FormulaC8 H6 Br N O
Name6-bromo-1,3-dihydro-2H-indol-2-one
ChEMBLCHEMBL2381492
DrugBank
ZINCZINC000002577874
PDB chain5akk Chain A Residue 1551 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5akk Successful Generation of Structural Information for Fragment-Based Drug Discovery.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		P371 M469 N472
Binding residue
(residue number reindexed from 1)		P367 M463 N466
Annotation score1
Binding affinityMOAD: ic50=99.3uM
PDBbind-CN: -logKd/Ki=4.00,IC50=99.3uM
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) F263 H330 D331 W332 N355 N374 Y379 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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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5akk, PDBe:5akk, PDBj:5akk
PDBsum5akk
PubMed25931264
UniProtP34913|HYES_HUMAN Bifunctional epoxide hydrolase 2 (Gene Name=EPHX2)

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