Structure of PDB 5aki Chain A Binding Site BS01

Receptor Information
>5aki Chain A (length=544) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TLRAAVFDLDGVLALPAVFGVLGRTEEALALPRGLLNDAFQKGGPEGATT
RLMKGEITLSQWIPLMEENCRKCSETAKVCLPSIKEIFDKAISARKINRP
MLQAALMLRKKGFTTAILTNTWLDDRAERDGLAQLMCELKMHFDFLIESC
QVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILVQ
DTDTALKELEKVTGIQLLNTPAPLPTSCNPSDMSHGYVTVKPRVRLHFVE
LGSGPAVCLCHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESSAPPE
IEEYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPERVRA
VASLNTPFIPANPNMSPLESIKANPVFDYQLYFQEPGVAEAELEQNLSRT
FKSLFRASDESVLSMHKVCEAGGLFVNSPEEPSLSRMVTEEEIQFYVQQF
KKSGFRGPLNWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLVPQMS
QHMEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDARN
Ligand information
Ligand ID6NF
InChIInChI=1S/C15H20N4/c1-2-4-12(5-3-1)11-17-15-10-14(18-19-15)13-6-8-16-9-7-13/h6-10,12H,1-5,11H2,(H2,17,18,19)
InChIKeyPAVOZTULRSGNJC-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1cnccc1c2cc(n[nH]2)NCC3CCCCC3
CACTVS 3.385C1CCC(CC1)CNc2cc([nH]n2)c3ccncc3
FormulaC15 H20 N4
NameN-(CYCLOHEXYLMETHYL)-3-(4-PYRIDYL)-1H-PYRAZOL-5-AMINE
ChEMBL
DrugBank
ZINCZINC000230472026
PDB chain5aki Chain A Residue 1558 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5aki Successful Generation of Structural Information for Fragment-Based Drug Discovery.
Resolution1.81 Å
Binding residue
(original residue number in PDB)		F267 D335 Y383 Q384 L408 M419 Y466
Binding residue
(residue number reindexed from 1)		F263 D331 Y379 Q380 L404 M415 Y462
Annotation score1
Binding affinityMOAD: ic50=0.754uM
PDBbind-CN: -logKd/Ki=6.12,IC50=0.754uM
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 Y462 D492 H520
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:5aki, PDBe:5aki, PDBj:5aki
PDBsum5aki
PubMed25931264
UniProtP34913|HYES_HUMAN Bifunctional epoxide hydrolase 2 (Gene Name=EPHX2)

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