sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2010-01-29
| Name: | Thiamine pyrophosphokinase |
|---|---|
| ID: | THIN_BACSU |
| AC: | O34664 |
| Organism: | Bacillus subtilis |
| Reign: | Bacteria |
| TaxID: | 224308 |
| EC Number: | 2.7.6.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 38 % |
| D | 62 % |
| B-Factor: | 36.799 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.715 | 1113.750 |
| % Hydrophobic | % Polar |
|---|---|
| 30.91 | 69.09 |
| According to VolSite | |
| HET Code: | VIB |
|---|---|
| Formula: | C12H17N4OS |
| Molecular weight: | 265.355 g/mol |
| DrugBank ID: | DB00152 |
| Buried Surface Area: | 63.57 % |
| 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 |
|---|---|---|
| 26.3598 | 6.50828 | -17.4061 |
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 |
| N4A | O | LYS- 77 | 2.83 | 130.59 | H-Bond (Ligand Donor) |
| N4A | OD2 | ASP- 78 | 3.24 | 140.13 | H-Bond (Ligand Donor) |
| CM2 | CD1 | LEU- 169 | 4.38 | 0 | Hydrophobic |
| CM2 | CB | TYR- 174 | 4.32 | 0 | Hydrophobic |
| CM4 | CE2 | TYR- 174 | 3.82 | 0 | Hydrophobic |
| C5A | CB | TYR- 174 | 3.86 | 0 | Hydrophobic |
| C5A | CD2 | TYR- 174 | 3.37 | 0 | Hydrophobic |
| CM2 | CD1 | LEU- 176 | 3.78 | 0 | Hydrophobic |
| CM2 | CG | LEU- 187 | 4.24 | 0 | Hydrophobic |
| CM2 | SG | CYS- 188 | 3.86 | 0 | Hydrophobic |
| CM4 | CB | SER- 190 | 3.91 | 0 | Hydrophobic |
| C7 | CB | SER- 190 | 4.3 | 0 | Hydrophobic |
| O1 | OG | SER- 190 | 2.73 | 161.16 | H-Bond (Protein Donor) |
