Structure of PDB 5lz9 Chain A Binding Site BS01

Receptor Information
>5lz9 Chain A (length=370) 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
WDCLIEGDDENLIPGTNINT
Ligand information
Ligand ID7BR
InChIInChI=1S/C19H23FN2O4S/c1-19(4-8-27(24,25)9-5-19)15-11-18(23)22(13-15)6-7-26-16-2-3-17(20)14(10-16)12-21/h2-3,10,15H,4-9,11,13H2,1H3/t15-/m1/s1
InChIKeySYEMWCXBADSSGE-OAHLLOKOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC1(CCS(=O)(=O)CC1)[C@@H]2CC(=O)N(C2)CCOc3ccc(c(c3)C#N)F
CACTVS 3.385CC1(CC[S](=O)(=O)CC1)[C@H]2CN(CCOc3ccc(F)c(c3)C#N)C(=O)C2
CACTVS 3.385CC1(CC[S](=O)(=O)CC1)[CH]2CN(CCOc3ccc(F)c(c3)C#N)C(=O)C2
OpenEye OEToolkits 2.0.6CC1(CCS(=O)(=O)CC1)C2CC(=O)N(C2)CCOc3ccc(c(c3)C#N)F
FormulaC19 H23 F N2 O4 S
Name2-fluoranyl-5-[2-[(4~{S})-4-[4-methyl-1,1-bis(oxidanylidene)thian-4-yl]-2-oxidanylidene-pyrrolidin-1-yl]ethoxy]benzenecarbonitrile
ChEMBLCHEMBL3922315
DrugBank
ZINCZINC000584905440
PDB chain5lz9 Chain A Residue 503 [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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PDB5lz9 Fragment-Based Approach to the Development of an Orally Bioavailable Lactam Inhibitor of Lipoprotein-Associated Phospholipase A2 (Lp-PLA2).
Resolution2.06 Å
Binding residue
(original residue number in PDB)		F110 G152 L153 G154 A155 S273 F274 W298 F322 H351 Q352 A355 F357
Binding residue
(residue number reindexed from 1)		F56 G98 L99 G100 A101 S219 F220 W244 F268 H297 Q298 A301 F303
Annotation score1
Binding affinityMOAD: ic50=0.12uM
PDBbind-CN: -logKd/Ki=6.92,IC50=0.12uM
BindingDB: IC50=32nM
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:5lz9, PDBe:5lz9, PDBj:5lz9
PDBsum5lz9
PubMed27933945
UniProtQ13093|PAFA_HUMAN Platelet-activating factor acetylhydrolase (Gene Name=PLA2G7)

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