Structure of PDB 5i9i Chain A Binding Site BS01

Receptor Information
>5i9i 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]
TKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEY
FWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGL
GAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSW
LYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKF
DMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLG
DEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQN
FADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFD
QWDCLIEGDDENLIPGTNINT
Ligand information
Ligand ID5HV
InChIInChI=1S/C36H38F4N4O2S/c1-3-42(4-2)20-21-43(22-25-8-12-27(13-9-25)28-14-16-29(17-15-28)36(38,39)40)33(45)23-44-32-7-5-6-31(32)34(46)41-35(44)47-24-26-10-18-30(37)19-11-26/h8-19H,3-7,20-24H2,1-2H3
InChIKeyWDPFJWLDPVQCAJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01CCN(CC)CCN(Cc2ccc(c1ccc(C(F)(F)F)cc1)cc2)C(=O)CN3C(=NC(C4=C3CCC4)=O)SCc5ccc(cc5)F
OpenEye OEToolkits 1.9.2CCN(CC)CCN(Cc1ccc(cc1)c2ccc(cc2)C(F)(F)F)C(=O)CN3C4=C(CCC4)C(=O)N=C3SCc5ccc(cc5)F
CACTVS 3.385CCN(CC)CCN(Cc1ccc(cc1)c2ccc(cc2)C(F)(F)F)C(=O)CN3C4=C(CCC4)C(=O)N=C3SCc5ccc(F)cc5
FormulaC36 H38 F4 N4 O2 S
NameN-[2-(diethylamino)ethyl]-2-{2-[(4-fluorobenzyl)sulfanyl]-4-oxo-4,5,6,7-tetrahydro-1H-cyclopenta[d]pyrimidin-1-yl}-N-{[ 4'-(trifluoromethyl)biphenyl-4-yl]methyl}acetamide;
Darapladib
ChEMBLCHEMBL204021
DrugBankDB06311
ZINCZINC000003842798
PDB chain5i9i Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5i9i Structural and Thermodynamic Characterization of Protein-Ligand Interactions Formed between Lipoprotein-Associated Phospholipase A2 and Inhibitors
Resolution2.7 Å
Binding residue
(original residue number in PDB)		F110 L111 L121 G152 L153 G154 L159 S273 F274 W298 H351 Q352 F357 L369 L371
Binding residue
(residue number reindexed from 1)		F57 L58 L68 G99 L100 G101 L106 S220 F221 W245 H298 Q299 F304 L316 L318
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.30,Kd=49.7nM
BindingDB: IC50=0.250000nM,Ki=110nM,Kd=5.0nM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5i9i, PDBe:5i9i, PDBj:5i9i
PDBsum5i9i
PubMed27078579
UniProtQ13093|PAFA_HUMAN Platelet-activating factor acetylhydrolase (Gene Name=PLA2G7)

[Back to BioLiP]