sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.790 Å
X-ray
2010-03-31
| Name: | Thiamin pyrophosphokinase family protein |
|---|---|
| ID: | Q82ZE3_ENTFA |
| AC: | Q82ZE3 |
| Organism: | Enterococcus faecalis |
| Reign: | Bacteria |
| TaxID: | 226185 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 41 % |
| D | 59 % |
| B-Factor: | 43.352 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.742 | 1765.125 |
| % Hydrophobic | % Polar |
|---|---|
| 30.78 | 69.22 |
| According to VolSite | |
| HET Code: | TPP |
|---|---|
| Formula: | C12H16N4O7P2S |
| Molecular weight: | 422.291 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61 % |
| Polar Surface area: | 225.32 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 3 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -3.69412 | 7.28919 | 61.5439 |
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 |
| N4' | OD1 | ASP- 76 | 3.42 | 0 | Ionic (Ligand Cationic) |
| S1 | CG2 | THR- 78 | 3.96 | 0 | Hydrophobic |
| C7 | CG2 | THR- 78 | 4.48 | 0 | Hydrophobic |
| O3A | N | ASP- 79 | 3.2 | 140.57 | H-Bond (Protein Donor) |
| O1B | OG1 | THR- 80 | 3.16 | 155.16 | H-Bond (Protein Donor) |
| CM2 | CD1 | LEU- 169 | 4.07 | 0 | Hydrophobic |
| C5' | CG | TYR- 174 | 4.18 | 0 | Hydrophobic |
| C7' | CE2 | TYR- 174 | 4.03 | 0 | Hydrophobic |
| CM4 | CZ | TYR- 174 | 3.73 | 0 | Hydrophobic |
| CM2 | CD2 | LEU- 176 | 3.65 | 0 | Hydrophobic |
| CM2 | CG | TYR- 187 | 3.76 | 0 | Hydrophobic |
| C7' | CB | SER- 189 | 4.31 | 0 | Hydrophobic |
| CM4 | CB | SER- 189 | 3.65 | 0 | Hydrophobic |
| C5 | CB | SER- 189 | 3.78 | 0 | Hydrophobic |
| O2A | MG | MG- 223 | 2.4 | 0 | Metal Acceptor |
