Structure of PDB 5ye9 Chain A Binding Site BS01

Receptor Information
>5ye9 Chain A (length=369) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQLDTLWIPNKEYFWGLS
KFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRT
LYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRT
LKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQL
KDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYS
RIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFT
FATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCL
IEGDDENLIPGTNINTTNQ
Ligand information
Ligand ID8U6
InChIInChI=1S/C25H19N3O4S/c1-17(29)27-21-7-11-24(12-8-21)33(30,31)28-22-9-13-25(20(14-22)16-26)32-23-10-6-18-4-2-3-5-19(18)15-23/h2-15,28H,1H3,(H,27,29)
InChIKeyXLRISFAORWYVBT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(=O)Nc1ccc(cc1)[S](=O)(=O)Nc2ccc(Oc3ccc4ccccc4c3)c(c2)C#N
OpenEye OEToolkits 2.0.6CC(=O)Nc1ccc(cc1)S(=O)(=O)Nc2ccc(c(c2)C#N)Oc3ccc4ccccc4c3
FormulaC25 H19 N3 O4 S
NameN-[4-[(3-cyano-4-naphthalen-2-yloxy-phenyl)sulfamoyl]phenyl]ethanamide
ChEMBLCHEMBL4075815
DrugBank
ZINC
PDB chain5ye9 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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PDB5ye9 Structure-Guided Discovery of Novel, Potent, and Orally Bioavailable Inhibitors of Lipoprotein-Associated Phospholipase A2.
Resolution1.876 Å
Binding residue
(original residue number in PDB)		L107 F110 L153 G154 A155 H272 S273 Q352 A355 F357
Binding residue
(residue number reindexed from 1)		L49 F52 L95 G96 A97 H214 S215 Q294 A297 F299
Annotation score1
Binding affinityMOAD: ic50=355nM
PDBbind-CN: -logKd/Ki=6.45,IC50=355nM
BindingDB: IC50=355nM
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:5ye9, PDBe:5ye9, PDBj:5ye9
PDBsum5ye9
PubMed29193967
UniProtQ13093|PAFA_HUMAN Platelet-activating factor acetylhydrolase (Gene Name=PLA2G7)

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