Structure of PDB 5vfn Chain A Binding Site BS01

Receptor Information
>5vfn Chain A (length=121) Species: 1042543 (Bothrops pauloensis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGQPKDATDRCCYVHKCC
YKKLTGCDPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENL
GTYNKKYRYHLKPFCKKADPC
Ligand information
Ligand IDHCI
InChIInChI=1S/C9H10O2/c10-9(11)7-6-8-4-2-1-3-5-8/h1-5H,6-7H2,(H,10,11)
InChIKeyXMIIGOLPHOKFCH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)CCc1ccccc1
OpenEye OEToolkits 1.7.6c1ccc(cc1)CCC(=O)O
CACTVS 3.370OC(=O)CCc1ccccc1
FormulaC9 H10 O2
NameHYDROCINNAMIC ACID;
3PP;
3-PHENYLPROPIONIC ACID
ChEMBLCHEMBL851
DrugBankDB02024
ZINCZINC000000154564
PDB chain5vfn Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5vfn Structural studies with BnSP-7 reveal an atypical oligomeric conformation compared to phospholipases A2-like toxins.
Resolution2.389 Å
Binding residue
(original residue number in PDB)		K16 K20 K115 R118
Binding residue
(residue number reindexed from 1)		K15 K19 K105 R108
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.52,Kd=300uM
Enzymatic activity
Catalytic site (original residue number in PDB) N28 G30 L32 H48 K49 Y52 Y73 D99
Catalytic site (residue number reindexed from 1) N27 G29 L31 H47 K48 Y51 Y64 D89
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004623 phospholipase A2 activity
GO:0005509 calcium ion binding
GO:0005543 phospholipid binding
GO:0047498 calcium-dependent phospholipase A2 activity
GO:0090729 toxin activity
Biological Process
GO:0006644 phospholipid metabolic process
GO:0016042 lipid catabolic process
GO:0035821 modulation of process of another organism
GO:0042130 negative regulation of T cell proliferation
GO:0042742 defense response to bacterium
GO:0050482 arachidonate secretion
Cellular Component
GO:0005576 extracellular region

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Cellular Component
External links
PDB RCSB:5vfn, PDBe:5vfn, PDBj:5vfn
PDBsum5vfn
PubMed28751219
UniProtQ9IAT9|PA2H_BOTPA Basic phospholipase A2 homolog BnSP-7

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