Structure of PDB 5akl Chain A Binding Site BS01

Receptor Information
>5akl Chain A (length=534) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TLRAAVFDLDGVLALPAVFGVLGRTEEALALPRGLLNDAFQKGGPEGATT
RLMKGEITLSQWIPLMEENCRKFSIKEIFDKAISARKINRPMLQAALMLR
KKGFTTAILTNTWLDDRAERDGLAQLMCELKMHFDFLIESCQVGMVKPEP
QIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILVQDTDTALKEL
EKVTGIQLLNTPAPLPTSCNPSDMSHGYVTVKPRVRLHFVELGSGPAVCL
CHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESSAPPEIEEYCMEVL
CKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPERVRAVASLNTPFI
PANPNMSPLESIKANPVFDYQLYFQEPGVAEAELEQNLSRTFKSLFRASD
ESVLSMHKVCEAGGLFVNSPEEPSLSRMVTEEEIQFYVQQFKKSGFRGPL
NWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLVPQMSQHMEDWIPH
LKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDAR
Ligand information
Ligand ID6N8
InChIInChI=1S/C20H20N2O/c23-20(22-15-7-8-16-22)21-14-13-19(17-9-3-1-4-10-17)18-11-5-2-6-12-18/h1-12,15-16,19H,13-14H2,(H,21,23)
InChIKeyHEHFNRQOOMVVBY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O=C(NCCC(c1ccccc1)c2ccccc2)n3cccc3
OpenEye OEToolkits 1.7.6c1ccc(cc1)C(CCNC(=O)n2cccc2)c3ccccc3
FormulaC20 H20 N2 O
NameN-(3,3-DIPHENYLPROPYL)PYRROLIDINE-1-CARBOXAMIDE
ChEMBL
DrugBank
ZINCZINC000230472086
PDB chain5akl 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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PDB5akl Successful Generation of Structural Information for Fragment-Based Drug Discovery.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		F267 D335 W336 Y383 L408 M419 Y466 V498 H524
Binding residue
(residue number reindexed from 1)		F254 D322 W323 Y370 L395 M406 Y453 V485 H511
Annotation score1
Binding affinityMOAD: ic50<0.086uM
PDBbind-CN: -logKd/Ki=7.07,IC50<0.086uM
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) F254 H321 D322 W323 N346 N365 Y370 Y453 D483 H511
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:5akl, PDBe:5akl, PDBj:5akl
PDBsum5akl
PubMed25931264
UniProtP34913|HYES_HUMAN Bifunctional epoxide hydrolase 2 (Gene Name=EPHX2)

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