Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3f10

2.300 Å

X-ray

2008-10-27

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:8-oxoguanine-DNA-glycosylase
ID:Q97FM4_CLOAB
AC:Q97FM4
Organism:Clostridium acetobutylicum
Reign:Bacteria
TaxID:272562
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:29.136
Number of residues:28
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.530506.250

% Hydrophobic% Polar
40.6759.33
According to VolSite

Ligand :
3f10_1 Structure
HET Code: 8HG
Formula: C10H13N5O5
Molecular weight: 283.241 g/mol
DrugBank ID: DB02502
Buried Surface Area:71.99 %
Polar Surface area: 149.51 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 5
Rings: 3
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
28.197-12.0312-11.3477


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
N7OGLY- 302.83167.83H-Bond
(Ligand Donor)
C2'CBSER- 1253.810Hydrophobic
C5'CD1ILE- 1303.620Hydrophobic
C5'CD1ILE- 1334.420Hydrophobic
N2OPRO- 2393.25125.73H-Bond
(Ligand Donor)
N2OD2ASP- 2413.23122.91H-Bond
(Ligand Donor)
N1OE1GLN- 2783.32142.77H-Bond
(Ligand Donor)
N2OE1GLN- 2783.24149.36H-Bond
(Ligand Donor)
O6NE2GLN- 2793.25167.5H-Bond
(Protein Donor)
O5'NH1ARG- 2863.19128.17H-Bond
(Protein Donor)