Structure of PDB 2qvd Chain A Binding Site BS01

Receptor Information
>2qvd 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 IDBER
InChIInChI=1S/C20H18NO4/c1-22-17-4-3-12-7-16-14-9-19-18(24-11-25-19)8-13(14)5-6-21(16)10-15(12)20(17)23-2/h3-4,7-10H,5-6,11H2,1-2H3/q+1
InChIKeyYBHILYKTIRIUTE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0COc1ccc2cc-3[n+](cc2c1OC)CCc4c3cc5c(c4)OCO5
ACDLabs 10.04O1c2c(OC1)cc5c(c2)c4cc3ccc(OC)c(OC)c3c[n+]4CC5
CACTVS 3.341COc1ccc2cc3c4cc5OCOc5cc4CC[n+]3cc2c1OC
FormulaC20 H18 N O4
NameBERBERINE
ChEMBLCHEMBL295124
DrugBankDB04115
ZINCZINC000003779067
PDB chain2qvd Chain A Residue 1811 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2qvd Identification of a novel and potent inhibitor of phospholipase A(2) in a medicinal plant: crystal structure at 1.93A and Surface Plasmon Resonance analysis of phospholipase A(2) complexed with berberine
Resolution1.93 Å
Binding residue
(original residue number in PDB)		F5 A18 I19 G30 F106
Binding residue
(residue number reindexed from 1)		F5 A17 I18 G29 F96
Annotation score1
Binding affinityMOAD: Kd=0.000000064M
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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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2qvd, PDBe:2qvd, PDBj:2qvd
PDBsum2qvd
PubMed21420512
UniProtP59071|PA2B8_DABRR Basic phospholipase A2 VRV-PL-VIIIa

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