sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 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: | 19.497 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.824 | 459.000 |
| % Hydrophobic | % Polar |
|---|---|
| 54.41 | 45.59 |
| According to VolSite | |
| HET Code: | THM |
|---|---|
| Formula: | C10H14N2O5 |
| Molecular weight: | 242.229 g/mol |
| DrugBank ID: | DB04485 |
| Buried Surface Area: | 68.71 % |
| 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: | 2 |
| X | Y | Z |
|---|---|---|
| 20.2495 | 21.8421 | 9.67065 |
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 |
| C5' | CB | HIS- 58 | 4.41 | 0 | Hydrophobic |
| C3' | CB | HIS- 58 | 3.56 | 0 | Hydrophobic |
| C5' | CZ3 | TRP- 88 | 4.23 | 0 | Hydrophobic |
| C5M | CH2 | TRP- 88 | 4.24 | 0 | Hydrophobic |
| C4' | CD1 | ILE- 97 | 4.05 | 0 | Hydrophobic |
| O3' | OH | TYR- 101 | 2.52 | 146.21 | H-Bond (Protein Donor) |
| C1' | CE | MET- 128 | 4.4 | 0 | Hydrophobic |
| C5M | CE2 | TYR- 132 | 4 | 0 | Hydrophobic |
| C5M | CD | ARG- 163 | 3.53 | 0 | Hydrophobic |
| C5M | CB | ALA- 167 | 4.36 | 0 | Hydrophobic |
| C5M | CD1 | TYR- 172 | 4.1 | 0 | Hydrophobic |
| C2' | CE2 | TYR- 172 | 3.49 | 0 | Hydrophobic |
