Structure of PDB 3f98 Chain C Binding Site BS01

Receptor Information
>3f98 Chain C (length=377) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASFGQTKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWI
PNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVV
FSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEI
GDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNA
LDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAW
MFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRG
SVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGL
HKDFDQWDCLIEGDDENLIPGTNINTT
Ligand information
Ligand IDNTJ
InChIInChI=1S/C4H12NO2P/c1-4-7-8(6)5(2)3/h8H,4H2,1-3H3
InChIKeyVJBIKDDUGQICEU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCOP(=O)N(C)C
ACDLabs 10.04O=P(OCC)N(C)C
CACTVS 3.341
OpenEye OEToolkits 1.5.0		CCO[P@H](=O)N(C)C
CACTVS 3.341CCO[PH](=O)N(C)C
FormulaC4 H12 N O2 P
NameR-ETHYL N,N-DIMETHYLPHOSPHONAMIDATE
ChEMBL
DrugBank
ZINCZINC000038424911
PDB chain3f98 Chain C Residue 473 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3f98 Crystal structures of human group-VIIA phospholipase A2 inhibited by organophosphorus nerve agents exhibit non-aged complexes.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		G152 L153 S273 F274 W298 F322 H351
Binding residue
(residue number reindexed from 1)		G104 L105 S225 F226 W250 F274 H303
Annotation score1
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:3f98, PDBe:3f98, PDBj:3f98
PDBsum3f98
PubMed19394314
UniProtQ13093|PAFA_HUMAN Platelet-activating factor acetylhydrolase (Gene Name=PLA2G7)

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