Structure of PDB 5ye8 Chain A Binding Site BS01

Receptor Information
>5ye8 Chain A (length=366) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQRLDTLWIPNKEYFWGL
SKFLGTLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTL
YSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTL
KQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLK
DSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSR
IPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTF
ATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLI
EGDDENLIPGTNINTT
Ligand information
Ligand ID8U3
InChIInChI=1S/C7H7F2NO2S/c1-13(11,12)10-5-2-3-6(8)7(9)4-5/h2-4,10H,1H3
InChIKeyCRLGPRNTBCRIBM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[S](=O)(=O)Nc1ccc(F)c(F)c1
OpenEye OEToolkits 2.0.6CS(=O)(=O)Nc1ccc(c(c1)F)F
FormulaC7 H7 F2 N O2 S
NameN-[3,4-bis(fluoranyl)phenyl]methanesulfonamide
ChEMBLCHEMBL4076637
DrugBank
ZINCZINC000000029686
PDB chain5ye8 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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PDB5ye8 Structure-Guided Discovery of Novel, Potent, and Orally Bioavailable Inhibitors of Lipoprotein-Associated Phospholipase A2.
Resolution1.851 Å
Binding residue
(original residue number in PDB)		L107 L153 G154 A155 L159 H272 S273 Q352 F357
Binding residue
(residue number reindexed from 1)		L50 L94 G95 A96 L100 H213 S214 Q293 F298
Annotation score1
Binding affinityMOAD: ic50~1mM
PDBbind-CN: -logKd/Ki=3.00,IC50~1mM
BindingDB: IC50=1000000nM
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:5ye8, PDBe:5ye8, PDBj:5ye8
PDBsum5ye8
PubMed29193967
UniProtQ13093|PAFA_HUMAN Platelet-activating factor acetylhydrolase (Gene Name=PLA2G7)

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