sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2001-04-16
| Name: | Thiamine pyrophosphokinase |
|---|---|
| ID: | THI80_YEAST |
| AC: | P35202 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | 2.7.6.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 46 % |
| B | 54 % |
| B-Factor: | 23.092 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.365 | 550.125 |
| % Hydrophobic | % Polar |
|---|---|
| 23.93 | 76.07 |
| According to VolSite | |
| HET Code: | VIB |
|---|---|
| Formula: | C12H17N4OS |
| Molecular weight: | 265.355 g/mol |
| DrugBank ID: | DB00152 |
| Buried Surface Area: | 66.19 % |
| Polar Surface area: | 104.15 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 47.4498 | 30.9164 | 22.4067 |
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 |
| CM2 | SG | CYS- 5 | 3.98 | 0 | Hydrophobic |
| N4A | O | GLN- 122 | 2.98 | 150.79 | H-Bond (Ligand Donor) |
| CM4 | CB | GLN- 122 | 4.11 | 0 | Hydrophobic |
| S1 | CG2 | THR- 125 | 3.82 | 0 | Hydrophobic |
| CM2 | CB | TRP- 270 | 4.2 | 0 | Hydrophobic |
| CM4 | CH2 | TRP- 270 | 3.6 | 0 | Hydrophobic |
| C5A | CB | TRP- 270 | 4.23 | 0 | Hydrophobic |
| CM2 | CG1 | VAL- 272 | 3.7 | 0 | Hydrophobic |
| CM2 | CZ2 | TRP- 275 | 3.73 | 0 | Hydrophobic |
| CM2 | CB | SER- 285 | 4.14 | 0 | Hydrophobic |
| N1A | OG | SER- 285 | 2.67 | 168.65 | H-Bond (Protein Donor) |
| CM4 | CB | SER- 287 | 3.73 | 0 | Hydrophobic |
| C7 | CB | SER- 287 | 3.82 | 0 | Hydrophobic |
| O1 | OG | SER- 287 | 3.42 | 166.82 | H-Bond (Protein Donor) |
| O1 | O | HOH- 1011 | 2.97 | 162.17 | H-Bond (Protein Donor) |
