Structure of PDB 5jan Chain A Binding Site BS01

Receptor Information
>5jan 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 ID6HP
InChIInChI=1S/C10H16N2O3/c1-7(2)6-15-9-5-8(13)11(3)10(14)12(9)4/h5,7H,6H2,1-4H3
InChIKeyNBDGERYKSQRETJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)COC1=CC(=O)N(C)C(=O)N1C
ACDLabs 12.01CC(COC=1N(C(=O)N(C(C=1)=O)C)C)C
OpenEye OEToolkits 2.0.4CC(C)COC1=CC(=O)N(C(=O)N1C)C
FormulaC10 H16 N2 O3
Name1,3-dimethyl-6-(2-methylpropoxy)pyrimidine-2,4(1H,3H)-dione
ChEMBLCHEMBL3819543
DrugBank
ZINCZINC000584904749
PDB chain5jan 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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PDB5jan Exploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Discovered through X-ray Fragment Screening.
Resolution2.12 Å
Binding residue
(original residue number in PDB)		L153 E214 W298 F322
Binding residue
(residue number reindexed from 1)		L99 E160 W244 F268
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.01,Kd=980uM
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:5jan, PDBe:5jan, PDBj:5jan
PDBsum5jan
PubMed27167608
UniProtQ13093|PAFA_HUMAN Platelet-activating factor acetylhydrolase (Gene Name=PLA2G7)

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