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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

2oth

2.900 Å

X-ray

2007-02-08

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Basic phospholipase A2 VRV-PL-VIIIa
ID:PA2B8_DABRR
AC:P59071
Organism:Daboia russelii
Reign:Eukaryota
TaxID:31159
EC Number:3.1.1.4


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:28.458
Number of residues:14
Including
Standard Amino Acids: 13
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.913469.125

% Hydrophobic% Polar
61.1538.85
According to VolSite

Ligand :
2oth_1 Structure
HET Code: NIM
Formula: C13H12N2O5S
Molecular weight: 308.310 g/mol
DrugBank ID: DB04743
Buried Surface Area:25.96 %
Polar Surface area: 109.6 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 1
Rings: 2
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
33.46795.105-9.58038


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
C1CD2LEU- 23.30Hydrophobic
C9CD2LEU- 24.480Hydrophobic
C7CD2LEU- 23.620Hydrophobic
C4CG1ILE- 194.410Hydrophobic
C6CD1ILE- 193.20Hydrophobic
C13CD1ILE- 193.930Hydrophobic
C4CBSER- 233.790Hydrophobic
O2NZLYS- 693.24166.99H-Bond
(Protein Donor)
C1CDLYS- 6940Hydrophobic