Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

4bdh

2.700 Å

X-ray

2012-10-05

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Serine/threonine-protein kinase Chk2
ID:CHK2_HUMAN
AC:O96017
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.11.1


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:68.731
Number of residues:19
Including
Standard Amino Acids: 19
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.993492.750

% Hydrophobic% Polar
57.5342.47
According to VolSite

Ligand :
4bdh_1 Structure
HET Code: WVI
Formula: C8H9N3S
Molecular weight: 179.242 g/mol
DrugBank ID: -
Buried Surface Area:52.56 %
Polar Surface area: 82.94 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 2
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
-37.606633.35898.1535


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
S11CG1VAL- 2343.790Hydrophobic
C1CBALA- 2474.140Hydrophobic
C1CD1LEU- 3013.580Hydrophobic
N7OGLU- 3022.96163.48H-Bond
(Ligand Donor)
N3OMET- 3043.27147.36H-Bond
(Ligand Donor)
NNMET- 3042.84155.99H-Bond
(Protein Donor)
C1CD1LEU- 3544.010Hydrophobic