Structure of PDB 5i8p Chain A Binding Site BS01

Receptor Information
>5i8p 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]
TKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEY
FWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGL
GAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSW
LYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKF
DMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLG
DEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQN
FADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFD
QWDCLIEGDDENLIPGTNI
Ligand information
Ligand IDVQ7
InChIInChI=1S/C23H19ClF5N3O5S/c1-31-20(32-4-6-38(34,35)7-5-32)11-19(30-22(31)33)36-12-13-8-17(25)21(18(26)9-13)37-14-2-3-16(24)15(10-14)23(27,28)29/h2-3,8-11H,4-7,12H2,1H3
InChIKeyFLCSHCSBIFPQJJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4CN1C(=CC(=NC1=O)OCc2cc(c(c(c2)F)Oc3ccc(c(c3)C(F)(F)F)Cl)F)N4CCS(=O)(=O)CC4
CACTVS 3.385CN1C(=O)N=C(OCc2cc(F)c(Oc3ccc(Cl)c(c3)C(F)(F)F)c(F)c2)C=C1N4CC[S](=O)(=O)CC4
FormulaC23 H19 Cl F5 N3 O5 S
Name6-[1,1-bis(oxidanylidene)-1,4-thiazinan-4-yl]-4-[[4-[4-chloranyl-3-(trifluoromethyl)phenoxy]-3,5-bis(fluoranyl)phenyl]methoxy]-1-methyl-pyrimidin-2-one
ChEMBLCHEMBL3792924
DrugBank
ZINCZINC000584905732
PDB chain5i8p 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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PDB5i8p Structural and Thermodynamic Characterization of Protein-Ligand Interactions Formed between Lipoprotein-Associated Phospholipase A2 and Inhibitors
Resolution2.37 Å
Binding residue
(original residue number in PDB)		F110 L121 G152 L153 L159 S273 F274 W298 F322 H351 Q352 A355 F357 L371
Binding residue
(residue number reindexed from 1)		F57 L68 G99 L100 L106 S220 F221 W245 F269 H298 Q299 A302 F304 L318
Annotation score1
Binding affinityMOAD: Kd=0.000000064M
PDBbind-CN: -logKd/Ki=6.73,Kd=185nM
BindingDB: Kd=1.9nM,IC50=1.7nM
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:5i8p, PDBe:5i8p, PDBj:5i8p
PDBsum5i8p
PubMed27078579
UniProtQ13093|PAFA_HUMAN Platelet-activating factor acetylhydrolase (Gene Name=PLA2G7)

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