sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2012-10-24
| Name: | Thymidylate kinase |
|---|---|
| ID: | Q8I4S1_PLAF7 |
| AC: | Q8I4S1 |
| Organism: | Plasmodium falciparum |
| Reign: | Eukaryota |
| TaxID: | 36329 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 14.896 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.614 | 297.000 |
| % Hydrophobic | % Polar |
|---|---|
| 65.91 | 34.09 |
| According to VolSite | |
| HET Code: | 74X |
|---|---|
| Formula: | C18H18ClF3N4O4S |
| Molecular weight: | 478.873 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.72 % |
| Polar Surface area: | 135.02 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 12.9433 | 8.41532 | 32.4791 |
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 |
| CAA | CB | PHE- 44 | 3.82 | 0 | Hydrophobic |
| FAF | CD | ARG- 47 | 3.31 | 0 | Hydrophobic |
| SAE | CD2 | LEU- 59 | 4.05 | 0 | Hydrophobic |
| CAL | CD1 | LEU- 59 | 4.27 | 0 | Hydrophobic |
| FAF | CD1 | LEU- 59 | 3.8 | 0 | Hydrophobic |
| CAO | CD2 | LEU- 59 | 3.76 | 0 | Hydrophobic |
| FAG | CB | LEU- 59 | 3.31 | 0 | Hydrophobic |
| CLA | CG | LYS- 60 | 3.72 | 0 | Hydrophobic |
| FAG | CG | LYS- 60 | 3.28 | 0 | Hydrophobic |
| CAA | CD1 | PHE- 74 | 4.01 | 0 | Hydrophobic |
| CAO | CZ | PHE- 74 | 3.86 | 0 | Hydrophobic |
| OAB | NH2 | ARG- 78 | 3.42 | 126.15 | H-Bond (Protein Donor) |
| OAB | NH1 | ARG- 78 | 2.67 | 160.67 | H-Bond (Protein Donor) |
| CAA | CB | ARG- 99 | 3.98 | 0 | Hydrophobic |
| CBB | CD | ARG- 99 | 3.94 | 0 | Hydrophobic |
| CAA | CB | SER- 103 | 3.93 | 0 | Hydrophobic |
| CBC | CD2 | TYR- 107 | 3.74 | 0 | Hydrophobic |
| SAE | CG2 | ILE- 152 | 3.73 | 0 | Hydrophobic |
| CAO | CE2 | TYR- 153 | 4.15 | 0 | Hydrophobic |
| SAE | CD2 | TYR- 153 | 4.2 | 0 | Hydrophobic |
