sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2016-01-31
| Name: | Thymidine kinase, putative |
|---|---|
| ID: | Q38CF2_TRYB2 |
| AC: | Q38CF2 |
| Organism: | Trypanosoma brucei brucei |
| Reign: | Eukaryota |
| TaxID: | 185431 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 56.577 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.702 | 610.875 |
| % Hydrophobic | % Polar |
|---|---|
| 46.41 | 53.59 |
| According to VolSite | |
| HET Code: | THM |
|---|---|
| Formula: | C10H14N2O5 |
| Molecular weight: | 242.229 g/mol |
| DrugBank ID: | DB04485 |
| Buried Surface Area: | 76.03 % |
| 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 |
|---|---|---|
| -15.3814 | -18.9819 | -12.6569 |
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' | CG | MET- 214 | 4.03 | 0 | Hydrophobic |
| C3' | CE | MET- 214 | 4.02 | 0 | Hydrophobic |
| C2' | SD | MET- 214 | 3.91 | 0 | Hydrophobic |
| C5M | SD | MET- 214 | 4.35 | 0 | Hydrophobic |
| O5' | OE1 | GLU- 286 | 2.98 | 132.57 | H-Bond (Ligand Donor) |
| O5' | OE2 | GLU- 286 | 2.6 | 155.59 | H-Bond (Ligand Donor) |
| C1' | CZ | PHE- 289 | 3.82 | 0 | Hydrophobic |
| C4' | CZ | PHE- 289 | 3.54 | 0 | Hydrophobic |
| C5M | CD1 | LEU- 312 | 3.8 | 0 | Hydrophobic |
| C5' | CD1 | LEU- 312 | 3.7 | 0 | Hydrophobic |
| O4 | N | TYR- 316 | 2.93 | 145.43 | H-Bond (Protein Donor) |
| C5M | CB | TYR- 316 | 4.32 | 0 | Hydrophobic |
| C5M | CG2 | THR- 352 | 3.74 | 0 | Hydrophobic |
| N3 | O | ARG- 361 | 2.84 | 156.48 | H-Bond (Ligand Donor) |
| O2 | N | LEU- 363 | 2.89 | 167.64 | H-Bond (Protein Donor) |
| O3' | N | GLY- 365 | 3.09 | 167.32 | H-Bond (Protein Donor) |
| C2' | CE2 | TYR- 370 | 3.39 | 0 | Hydrophobic |
| C1' | CZ | TYR- 370 | 4.23 | 0 | Hydrophobic |
| C5M | CE1 | TYR- 370 | 3.86 | 0 | Hydrophobic |
| O3' | O | HOH- 2022 | 2.55 | 171.33 | H-Bond (Ligand Donor) |
