Structure of PDB 4qf8 Chain A Binding Site BS01

Receptor Information
>4qf8 Chain A (length=121) Species: 97228 (Daboia russelii pulchella) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLLEFGKMILEETGKLAIPSYSSYGCYCGWGGKGTPKDATDRCCFVHDCC
YGNLPDCNPKSDRYKYKRVNGAIVCEKGTSCENRICECDKAAAICFRQNL
NTYSKKYMLYPDFLCKGELKC
Ligand information
Ligand IDSPD
InChIInChI=1S/C7H19N3/c8-4-1-2-6-10-7-3-5-9/h10H,1-9H2
InChIKeyATHGHQPFGPMSJY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(CCNCCCN)CN
ACDLabs 10.04NCCCNCCCCN
CACTVS 3.341NCCCCNCCCN
FormulaC7 H19 N3
NameSPERMIDINE;
N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE;
PA(34)
ChEMBLCHEMBL19612
DrugBankDB03566
ZINCZINC000001532612
PDB chain4qf8 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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PDB4qf8 Structures and binding studies of the complexes of phospholipase A2 with five inhibitors
Resolution1.65 Å
Binding residue
(original residue number in PDB)		A18 C29 G30 C45 H48 D49
Binding residue
(residue number reindexed from 1)		A17 C28 G29 C44 H47 D48
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.51,Kd=31nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y28 G30 G32 H48 D49 Y52 Y73 D99
Catalytic site (residue number reindexed from 1) Y27 G29 G31 H47 D48 Y51 Y64 D89
Enzyme Commision number 3.1.1.4: phospholipase A2.
Gene Ontology
Molecular Function
GO:0004623 phospholipase A2 activity
GO:0005509 calcium ion binding
GO:0005543 phospholipid binding
GO:0016787 hydrolase activity
GO:0046872 metal ion 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:0050482 arachidonate secretion
Cellular Component
GO:0005576 extracellular region

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Cellular Component
External links
PDB RCSB:4qf8, PDBe:4qf8, PDBj:4qf8
PDBsum4qf8
PubMed25541253
UniProtP59071|PA2B8_DABRR Basic phospholipase A2 VRV-PL-VIIIa

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