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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

2vqs

2.900 Å

X-ray

2008-03-18

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Deoxynucleoside kinase
ID:DNK_DROME
AC:Q9XZT6
Organism:Drosophila melanogaster
Reign:Eukaryota
TaxID:7227
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:47.888
Number of residues:28
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.189563.625

% Hydrophobic% Polar
55.6944.31
According to VolSite

Ligand :
2vqs_2 Structure
HET Code: BVD
Formula: C11H13BrN2O5
Molecular weight: 333.135 g/mol
DrugBank ID: DB03312
Buried Surface Area:74.53 %
Polar Surface area: 99.1 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 3
Rings: 2
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
11.3519-17.6629-6.50058


Binding mode :
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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
C2'CD1ILE- 294.210Hydrophobic
O5'OE1GLU- 522.62150.46H-Bond
(Ligand Donor)
O5'OE2GLU- 522.83135.43H-Bond
(Ligand Donor)
C5'CG2VAL- 544.110Hydrophobic
C5'CZ3TRP- 574.160Hydrophobic
C1'CD1LEU- 664.370Hydrophobic
O3'OHTYR- 702.94177.76H-Bond
(Protein Donor)
N3OE1GLN- 813.01137.53H-Bond
(Ligand Donor)
O4NE2GLN- 812.84157.34H-Bond
(Protein Donor)
BRCG1VAL- 843.910Hydrophobic
BRSDMET- 883.780Hydrophobic
BRCBARG- 1053.990Hydrophobic
BRCBALA- 1103.720Hydrophobic
C2'CE2PHE- 1143.930Hydrophobic