sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.910 Å
X-ray
2011-12-02
| Name: | Thymidylate kinase |
|---|---|
| ID: | KTHY_PSEAE |
| AC: | Q9HZN8 |
| Organism: | Pseudomonas aeruginosa |
| Reign: | Bacteria |
| TaxID: | 208964 |
| EC Number: | 2.7.4.9 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 24.716 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.122 | 435.375 |
| % Hydrophobic | % Polar |
|---|---|
| 69.77 | 30.23 |
| According to VolSite | |
| HET Code: | 0DF |
|---|---|
| Formula: | C13H11N3O |
| Molecular weight: | 225.246 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 82.82 % |
| Polar Surface area: | 45.23 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -7.14741 | -19.1677 | -26.4287 |
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 |
| C11 | CG | GLU- 12 | 3.86 | 0 | Hydrophobic |
| C7 | CB | GLU- 39 | 3.6 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 54 | 3.76 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 54 | 3.78 | 0 | Hydrophobic |
| C7 | SD | MET- 70 | 4.12 | 0 | Hydrophobic |
| C2 | CE | MET- 70 | 3.55 | 0 | Hydrophobic |
| O1 | NH2 | ARG- 74 | 2.85 | 165.75 | H-Bond (Protein Donor) |
| C7 | CB | ARG- 96 | 3.87 | 0 | Hydrophobic |
| C6 | CD | ARG- 96 | 3.56 | 0 | Hydrophobic |
| C5 | CD | ARG- 96 | 4.02 | 0 | Hydrophobic |
| DuAr | CZ | ARG- 96 | 3.79 | 5.82 | Pi/Cation |
| C7 | CB | ALA- 100 | 4.06 | 0 | Hydrophobic |
| C2 | CB | ALA- 100 | 3.76 | 0 | Hydrophobic |
| O1 | OG1 | THR- 101 | 2.54 | 150.49 | H-Bond (Protein Donor) |
| N3 | NE2 | GLN- 105 | 3.4 | 161.17 | H-Bond (Protein Donor) |
| N2 | OE1 | GLN- 105 | 2.61 | 159.69 | H-Bond (Ligand Donor) |
| C10 | CB | PHE- 155 | 3.85 | 0 | Hydrophobic |
