Structure of PDB 5jar Chain A Binding Site BS01

Receptor Information
>5jar 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 ID6HV
InChIInChI=1S/C18H15NOS/c1-12-5-3-4-6-15(12)16-11-14(8-7-13(16)2)17(20)18-19-9-10-21-18/h3-11H,1-2H3
InChIKeyWEOQMVQEKRDUIM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ccccc1c2cc(ccc2C)C(=O)c3sccn3
ACDLabs 12.01Cc1ccccc1c3c(ccc(C(=O)c2nccs2)c3)C
OpenEye OEToolkits 2.0.4Cc1ccccc1c2cc(ccc2C)C(=O)c3nccs3
FormulaC18 H15 N O S
Name(2',6-dimethyl[1,1'-biphenyl]-3-yl)(1,3-thiazol-2-yl)methanone
ChEMBLCHEMBL3819446
DrugBank
ZINCZINC000584904897
PDB chain5jar Chain A Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5jar Exploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Discovered through X-ray Fragment Screening.
Resolution2.11 Å
Binding residue
(original residue number in PDB)		L107 F110 L111 F125 G154 Q352 F357 L371
Binding residue
(residue number reindexed from 1)		L53 F56 L57 F71 G100 Q298 F303 L317
Annotation score1
Binding affinityMOAD: ic50=2uM
PDBbind-CN: -logKd/Ki=5.70,IC50=2.0uM
BindingDB: IC50=2000nM
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:5jar, PDBe:5jar, PDBj:5jar
PDBsum5jar
PubMed27167608
UniProtQ13093|PAFA_HUMAN Platelet-activating factor acetylhydrolase (Gene Name=PLA2G7)

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