Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

1bx9

2.600 Å

X-ray

1998-10-14

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
A100 %


Ligand binding site composition:

B-Factor:22.987
Number of residues:34
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.049398.250

% Hydrophobic% Polar
59.3240.68
According to VolSite

Ligand :
1bx9_1 Structure
HET Code: GLY_GGL_FOE
Formula: C21H28FN4O7S
Molecular weight: 499.533 g/mol
DrugBank ID: -
Buried Surface Area:45.06 %
Polar Surface area: 211.7 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 3
Rings: 1
Aromatic rings: 1
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 14

Mass center Coordinates

XYZ
16.803830.388421.4741


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
C1CBSER- 103.930Hydrophobic
CBCBSER- 104.070Hydrophobic
O3NILE- 113.35151.47H-Bond
(Protein Donor)
C7CD1ILE- 113.820Hydrophobic
CGCBALA- 123.950Hydrophobic
ONZLYS- 403.350Ionic
(Protein Cationic)
CGCBGLN- 524.20Hydrophobic
NOVAL- 532.85129.22H-Bond
(Ligand Donor)
ONVAL- 532.78163.97H-Bond
(Protein Donor)
CBCG2VAL- 533.60Hydrophobic
NOE2GLU- 653.050Ionic
(Ligand Cationic)
ONSER- 662.99165.88H-Bond
(Protein Donor)
OXTOGSER- 662.63151.04H-Bond
(Protein Donor)
OXTNH1ARG- 673.36125.77H-Bond
(Protein Donor)
C7CBSER- 1144.180Hydrophobic
C5CBPHE- 1184.350Hydrophobic
C5CZPHE- 1223.310Hydrophobic
OOHOH- 2533.08160.28H-Bond
(Protein Donor)