sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2005-10-10
| Name: | Thymidine kinase |
|---|---|
| ID: | KITH_UREPA |
| AC: | Q9PPP5 |
| Organism: | Ureaplasma parvum serovar 3 |
| Reign: | Bacteria |
| TaxID: | 273119 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 29.830 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.230 | 877.500 |
| % Hydrophobic | % Polar |
|---|---|
| 43.46 | 56.54 |
| According to VolSite | |
| HET Code: | THM |
|---|---|
| Formula: | C10H14N2O5 |
| Molecular weight: | 242.229 g/mol |
| DrugBank ID: | DB04485 |
| Buried Surface Area: | 75.14 % |
| 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 |
|---|---|---|
| 20.2848 | -15.6239 | 37.7234 |
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' | CE | MET- 21 | 4.37 | 0 | Hydrophobic |
| C5M | SD | MET- 21 | 4.23 | 0 | Hydrophobic |
| C3' | CE | MET- 21 | 3.92 | 0 | Hydrophobic |
| O5' | OE1 | GLU- 97 | 3.26 | 145.18 | H-Bond (Ligand Donor) |
| O5' | OE2 | GLU- 97 | 2.77 | 154.16 | H-Bond (Ligand Donor) |
| C4' | CZ | PHE- 100 | 3.95 | 0 | Hydrophobic |
| C1' | CZ | PHE- 100 | 3.89 | 0 | Hydrophobic |
| C5M | CD1 | LEU- 124 | 4.03 | 0 | Hydrophobic |
| C5' | CD1 | LEU- 124 | 3.75 | 0 | Hydrophobic |
| O4 | N | PHE- 128 | 2.69 | 143.75 | H-Bond (Protein Donor) |
| C5M | CB | PHE- 128 | 4.48 | 0 | Hydrophobic |
| C5M | CE1 | PHE- 133 | 4.32 | 0 | Hydrophobic |
| C5M | CB | SER- 163 | 3.62 | 0 | Hydrophobic |
| N3 | O | ILE- 178 | 2.59 | 168.84 | H-Bond (Ligand Donor) |
| O2 | N | LYS- 180 | 2.79 | 175.84 | H-Bond (Protein Donor) |
| O3' | N | GLY- 182 | 3.23 | 174.96 | H-Bond (Protein Donor) |
| C2' | CE2 | TYR- 187 | 3.53 | 0 | Hydrophobic |
| C1' | CZ | TYR- 187 | 4.37 | 0 | Hydrophobic |
| C5M | CE1 | TYR- 187 | 3.77 | 0 | Hydrophobic |
