sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.820 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 |
|---|---|
| A | 100 % |
| B-Factor: | 21.830 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.543 | 351.000 |
| % Hydrophobic | % Polar |
|---|---|
| 55.77 | 44.23 |
| According to VolSite | |
| HET Code: | 74W |
|---|---|
| Formula: | C18H18ClF3N4O4S |
| Molecular weight: | 478.873 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 69.05 % |
| 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 |
|---|---|---|
| 15.8735 | -4.7119 | 4.738 |
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 |
| OAD | OD2 | ASP- 17 | 2.77 | 163.32 | H-Bond (Ligand Donor) |
| FAG | CB | ASP- 17 | 3.36 | 0 | Hydrophobic |
| CAA | CB | PHE- 44 | 3.82 | 0 | Hydrophobic |
| SAE | CG | PRO- 45 | 4.3 | 0 | Hydrophobic |
| CBB | CD2 | LEU- 59 | 4.01 | 0 | Hydrophobic |
| CAA | CD1 | PHE- 74 | 4.14 | 0 | Hydrophobic |
| CBC | CZ | PHE- 74 | 4 | 0 | Hydrophobic |
| OAB | NH1 | ARG- 78 | 2.81 | 152.91 | H-Bond (Protein Donor) |
| CAA | CB | ARG- 99 | 3.89 | 0 | Hydrophobic |
| CAO | CD | ARG- 99 | 4.17 | 0 | Hydrophobic |
| CAA | CB | SER- 103 | 3.99 | 0 | Hydrophobic |
| CBC | CD2 | TYR- 107 | 4.28 | 0 | Hydrophobic |
| CAO | CE2 | TYR- 107 | 3.48 | 0 | Hydrophobic |
| CAL | CG | GLU- 151 | 4.38 | 0 | Hydrophobic |
| FAH | CB | GLU- 151 | 3.98 | 0 | Hydrophobic |
| CBC | CD2 | TYR- 153 | 4.16 | 0 | Hydrophobic |
| FAF | CB | TYR- 153 | 4.13 | 0 | Hydrophobic |
| CBA | CD2 | TYR- 153 | 4.37 | 0 | Hydrophobic |
| CL | CG | GLU- 154 | 3.51 | 0 | Hydrophobic |
| FAG | CG | GLU- 154 | 3.98 | 0 | Hydrophobic |
| FAH | CB | GLU- 154 | 3.55 | 0 | Hydrophobic |
| OAD | O | HOH- 2180 | 3.13 | 179.98 | H-Bond (Protein Donor) |
