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
2012-10-03
| Name: | Thymidylate kinase |
|---|---|
| ID: | KTHY_STAAN |
| AC: | P65249 |
| Organism: | Staphylococcus aureus |
| Reign: | Bacteria |
| TaxID: | 158879 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 24.251 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.309 | 394.875 |
| % Hydrophobic | % Polar |
|---|---|
| 52.99 | 47.01 |
| According to VolSite | |
| HET Code: | 14D |
|---|---|
| Formula: | C24H25F3N3O3 |
| Molecular weight: | 460.469 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.74 % |
| Polar Surface area: | 63.08 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 13.459 | -0.133909 | 3.22506 |
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 |
| F2 | CG | PRO- 38 | 4.4 | 0 | Hydrophobic |
| F3 | CG2 | ILE- 47 | 3.68 | 0 | Hydrophobic |
| C23 | CG | ARG- 48 | 3.65 | 0 | Hydrophobic |
| F2 | CB | ARG- 48 | 3.35 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 51 | 4.18 | 0 | Hydrophobic |
| F3 | CG2 | VAL- 51 | 3.26 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 52 | 3.74 | 0 | Hydrophobic |
| C1 | CD1 | PHE- 66 | 4.3 | 0 | Hydrophobic |
| C6 | CZ | PHE- 66 | 4.39 | 0 | Hydrophobic |
| F1 | CD1 | PHE- 66 | 3.48 | 0 | Hydrophobic |
| C24 | CB | SER- 69 | 3.73 | 0 | Hydrophobic |
| O2 | NH2 | ARG- 70 | 3.03 | 167.17 | H-Bond (Protein Donor) |
| C1 | CB | ARG- 92 | 3.86 | 0 | Hydrophobic |
| C7 | CD | ARG- 92 | 3.78 | 0 | Hydrophobic |
| C1 | CB | SER- 96 | 4.04 | 0 | Hydrophobic |
| O2 | OG | SER- 97 | 2.59 | 139.96 | H-Bond (Protein Donor) |
| C6 | CD1 | TYR- 100 | 4.04 | 0 | Hydrophobic |
| C7 | CZ | TYR- 100 | 3.79 | 0 | Hydrophobic |
| C8 | CE1 | TYR- 100 | 3.66 | 0 | Hydrophobic |
| O1 | NE2 | GLN- 101 | 2.84 | 160.13 | H-Bond (Protein Donor) |
| N2 | OE1 | GLN- 101 | 2.71 | 166.98 | H-Bond (Ligand Donor) |
