sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2000-05-23
| Name: | Thymidine kinase |
|---|---|
| ID: | KITH_HHV11 |
| AC: | P03176 |
| Organism: | Human herpesvirus 1 |
| Reign: | Viruses |
| TaxID: | 10299 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 30.177 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.964 | 479.250 |
| % Hydrophobic | % Polar |
|---|---|
| 65.49 | 34.51 |
| According to VolSite | |
| HET Code: | TMC |
|---|---|
| Formula: | C12H16N2O4 |
| Molecular weight: | 252.266 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 69.62 % |
| Polar Surface area: | 89.87 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 20.2707 | 21.8531 | 9.19911 |
Image generated by PoseView
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 |
| C10 | CB | HIS- 58 | 3.98 | 0 | Hydrophobic |
| C13 | CZ3 | TRP- 88 | 4.25 | 0 | Hydrophobic |
| C12 | CZ3 | TRP- 88 | 3.94 | 0 | Hydrophobic |
| C3 | CH2 | TRP- 88 | 4.06 | 0 | Hydrophobic |
| C13 | CG1 | ILE- 97 | 3.86 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 97 | 3.52 | 0 | Hydrophobic |
| C14 | CZ | PHE- 101 | 4.11 | 0 | Hydrophobic |
| C17 | CE2 | PHE- 101 | 4.44 | 0 | Hydrophobic |
| O7 | NE2 | GLN- 125 | 2.92 | 170.22 | H-Bond (Protein Donor) |
| N5 | OE1 | GLN- 125 | 2.93 | 178.51 | H-Bond (Ligand Donor) |
| C3 | CE | MET- 128 | 4.42 | 0 | Hydrophobic |
| C13 | CE | MET- 128 | 3.68 | 0 | Hydrophobic |
| C3 | CE2 | TYR- 132 | 4.24 | 0 | Hydrophobic |
| C3 | CD | ARG- 163 | 3.54 | 0 | Hydrophobic |
| C3 | CB | ALA- 167 | 4.46 | 0 | Hydrophobic |
| C3 | CD1 | TYR- 172 | 4.05 | 0 | Hydrophobic |
| C14 | CE2 | TYR- 172 | 3.67 | 0 | Hydrophobic |
