Structure of PDB 5jah Chain A Binding Site BS01

Receptor Information
>5jah 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 ID6HQ
InChIInChI=1S/C6H10N2O2/c1-6(2)4(9)7-5(10)8(6)3/h1-3H3,(H,7,9,10)
InChIKeyZNYIPTYJBRGSSL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4CC1(C(=O)NC(=O)N1C)C
ACDLabs 12.01
CACTVS 3.385		CN1C(=O)NC(=O)C1(C)C
FormulaC6 H10 N2 O2
Name1,5,5-trimethylimidazolidine-2,4-dione
ChEMBL
DrugBank
ZINCZINC000000393448
PDB chain5jah Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5jah Exploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Discovered through X-ray Fragment Screening.
Resolution2.06 Å
Binding residue
(original residue number in PDB)		G152 L153 S273 F274 W298 H351
Binding residue
(residue number reindexed from 1)		G98 L99 S219 F220 W244 H297
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.00,IC50>1mM
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:5jah, PDBe:5jah, PDBj:5jah
PDBsum5jah
PubMed27167608
UniProtQ13093|PAFA_HUMAN Platelet-activating factor acetylhydrolase (Gene Name=PLA2G7)

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