2.900 Å
X-ray
2008-03-18
Name: | Deoxynucleoside kinase |
---|---|
ID: | DNK_DROME |
AC: | Q9XZT6 |
Organism: | Drosophila melanogaster |
Reign: | Eukaryota |
TaxID: | 7227 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
B | 100 % |
B-Factor: | 47.888 |
---|---|
Number of residues: | 28 |
Including | |
Standard Amino Acids: | 28 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 0 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.189 | 563.625 |
% Hydrophobic | % Polar |
---|---|
55.69 | 44.31 |
According to VolSite |
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 |
X | Y | Z |
---|---|---|
11.3519 | -17.6629 | -6.50058 |
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
Ligand | Protein | Interaction | |||
---|---|---|---|---|---|
Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
C2' | CD1 | ILE- 29 | 4.21 | 0 | Hydrophobic |
O5' | OE1 | GLU- 52 | 2.62 | 150.46 | H-Bond (Ligand Donor) |
O5' | OE2 | GLU- 52 | 2.83 | 135.43 | H-Bond (Ligand Donor) |
C5' | CG2 | VAL- 54 | 4.11 | 0 | Hydrophobic |
C5' | CZ3 | TRP- 57 | 4.16 | 0 | Hydrophobic |
C1' | CD1 | LEU- 66 | 4.37 | 0 | Hydrophobic |
O3' | OH | TYR- 70 | 2.94 | 177.76 | H-Bond (Protein Donor) |
N3 | OE1 | GLN- 81 | 3.01 | 137.53 | H-Bond (Ligand Donor) |
O4 | NE2 | GLN- 81 | 2.84 | 157.34 | H-Bond (Protein Donor) |
BR | CG1 | VAL- 84 | 3.91 | 0 | Hydrophobic |
BR | SD | MET- 88 | 3.78 | 0 | Hydrophobic |
BR | CB | ARG- 105 | 3.99 | 0 | Hydrophobic |
BR | CB | ALA- 110 | 3.72 | 0 | Hydrophobic |
C2' | CE2 | PHE- 114 | 3.93 | 0 | Hydrophobic |