Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

5a4w

2.250 Å

X-ray

2015-06-15

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glutathione S-transferase F2
ID:GSTF2_ARATH
AC:P46422
Organism:Arabidopsis thaliana
Reign:Eukaryota
TaxID:3702
EC Number:2.5.1.18


Chains:

Chain Name:Percentage of Residues
within binding site
E46 %
F54 %


Ligand binding site composition:

B-Factor:33.640
Number of residues:37
Including
Standard Amino Acids: 37
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.937597.375

% Hydrophobic% Polar
53.1146.89
According to VolSite

Ligand :
5a4w_8 Structure
HET Code: QCT
Formula: C21H19O11
Molecular weight: 447.369 g/mol
DrugBank ID: -
Buried Surface Area:67.11 %
Polar Surface area: 189.2 Å2
Number of
H-Bond Acceptors: 11
H-Bond Donors: 6
Rings: 4
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 3

Mass center Coordinates

XYZ
8.00634-1.333789.55828


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
C13CGGLN- 734.440Hydrophobic
C7CBGLN- 733.210Hydrophobic
DuArDuArHIS- 773.670Aromatic Face/Face
O9OSER- 912.88166.56H-Bond
(Ligand Donor)
C26CBSER- 914.350Hydrophobic
C24CDLYS- 923.780Hydrophobic
C26CDLYS- 924.10Hydrophobic
C22CG1ILE- 943.810Hydrophobic
C21CD2TYR- 973.610Hydrophobic
C10CD1TYR- 973.330Hydrophobic
C14CBTYR- 974.060Hydrophobic
C10CBTYR- 974.080Hydrophobic
DuArDuArTYR- 973.810Aromatic Face/Face
C7CBALA- 1013.710Hydrophobic