Structure of PDB 5lyy Chain A Binding Site BS01

Receptor Information
>5lyy Chain A (length=371) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYF
WGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLG
AFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWL
YLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFD
MEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGD
EVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNF
ADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQ
WDCLIEGDDENLIPGTNINTT
Ligand information
Ligand ID7BJ
InChIInChI=1S/C16H19FN2O3/c17-12-4-6-13(7-5-12)22-11-10-19-14(20)16(18-15(19)21)8-2-1-3-9-16/h4-7H,1-3,8-11H2,(H,18,21)
InChIKeyWWRSQXLLQVERHE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Fc1ccc(OCCN2C(=O)NC3(CCCCC3)C2=O)cc1
OpenEye OEToolkits 2.0.6c1cc(ccc1OCCN2C(=O)C3(CCCCC3)NC2=O)F
FormulaC16 H19 F N2 O3
Name3-[2-(4-fluoranylphenoxy)ethyl]-1,3-diazaspiro[4.5]decane-2,4-dione
ChEMBLCHEMBL3908555
DrugBank
ZINC
PDB chain5lyy Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5lyy Fragment-Based Approach to the Development of an Orally Bioavailable Lactam Inhibitor of Lipoprotein-Associated Phospholipase A2 (Lp-PLA2).
Resolution2.17 Å
Binding residue
(original residue number in PDB)		F110 G152 L153 G154 L159 S273 F274 W298 F322 H351 Q352 F357
Binding residue
(residue number reindexed from 1)		F56 G98 L99 G100 L105 S219 F220 W244 F268 H297 Q298 F303
Annotation score1
Binding affinityMOAD: ic50=14uM
PDBbind-CN: -logKd/Ki=4.85,IC50=14uM
BindingDB: IC50=14000nM
Enzymatic activity
Enzyme Commision number 3.1.1.47: 1-alkyl-2-acetylglycerophosphocholine esterase.
Gene Ontology
Molecular Function
GO:0003847 1-alkyl-2-acetylglycerophosphocholine esterase activity
GO:0005515 protein binding
GO:0005543 phospholipid binding
GO:0016787 hydrolase activity
GO:0016788 hydrolase activity, acting on ester bonds
GO:0047499 calcium-independent phospholipase A2 activity
Biological Process
GO:0009395 phospholipid catabolic process
GO:0016486 peptide hormone processing
GO:0034374 low-density lipoprotein particle remodeling
GO:0034440 lipid oxidation
GO:0034441 plasma lipoprotein particle oxidation
GO:0034638 phosphatidylcholine catabolic process
GO:0046469 platelet activating factor metabolic process
GO:0050729 positive regulation of inflammatory response
GO:0062234 platelet activating factor catabolic process
GO:0090026 positive regulation of monocyte chemotaxis
Cellular Component
GO:0005576 extracellular region
GO:0034362 low-density lipoprotein particle
GO:0034364 high-density lipoprotein particle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5lyy, PDBe:5lyy, PDBj:5lyy
PDBsum5lyy
PubMed27933945
UniProtQ13093|PAFA_HUMAN Platelet-activating factor acetylhydrolase (Gene Name=PLA2G7)

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