Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

4hmb

2.210 Å

X-ray

2012-10-18

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Phospholipase A2 VRV-PL-VIIIa
ID:D0VX11_9SAUR
AC:D0VX11
Organism:Daboia russellii pulchella
Reign:Eukaryota
TaxID:97228
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:31.726
Number of residues:21
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.350391.500

% Hydrophobic% Polar
56.0343.97
According to VolSite

Ligand :
4hmb_1 Structure
HET Code: PZZ
Formula: C14H21N2O
Molecular weight: 233.329 g/mol
DrugBank ID: DB08447
Buried Surface Area:43.81 %
Polar Surface area: 40.46 Å2
Number of
H-Bond Acceptors: 1
H-Bond Donors: 3
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
22.27786.142947.40624


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
C8CGLEU- 24.330Hydrophobic
C4CD1LEU- 24.150Hydrophobic
C16CE2PHE- 53.90Hydrophobic
C5CBALA- 184.120Hydrophobic
C4CG1ILE- 194.290Hydrophobic
C8CBSER- 234.240Hydrophobic
C15CBCYS- 294.50Hydrophobic
C16SGCYS- 454.040Hydrophobic
C16CBHIS- 484.450Hydrophobic
O17ND1HIS- 483.12145.65H-Bond
(Ligand Donor)