sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.640 Å
X-ray
2012-10-22
| Name: | Glucose-1-phosphate thymidylyltransferase |
|---|---|
| ID: | Q9AGY4_ANETH |
| AC: | Q9AGY4 |
| Organism: | Aneurinibacillus thermoaerophilus |
| Reign: | Bacteria |
| TaxID: | 143495 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 83 % |
| B | 17 % |
| B-Factor: | 21.691 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.791 | 428.625 |
| % Hydrophobic | % Polar |
|---|---|
| 55.12 | 44.88 |
| According to VolSite | |
| HET Code: | THM |
|---|---|
| Formula: | C10H14N2O5 |
| Molecular weight: | 242.229 g/mol |
| DrugBank ID: | DB04485 |
| Buried Surface Area: | 63.02 % |
| Polar Surface area: | 99.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -44.7459 | 8.62124 | -18.8672 |
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 |
| C5M | CD2 | LEU- 43 | 4.3 | 0 | Hydrophobic |
| C2' | CD1 | LEU- 43 | 3.57 | 0 | Hydrophobic |
| C1' | CE2 | TYR- 112 | 3.7 | 0 | Hydrophobic |
| C4' | CE2 | TYR- 112 | 3.56 | 0 | Hydrophobic |
| O3' | N | GLY- 113 | 3.08 | 160.48 | H-Bond (Protein Donor) |
| C3' | CB | PHE- 116 | 4.04 | 0 | Hydrophobic |
| C2' | CG2 | THR- 117 | 4.38 | 0 | Hydrophobic |
| C1' | CD | ARG- 217 | 4.34 | 0 | Hydrophobic |
| C4' | CG | ARG- 217 | 4.05 | 0 | Hydrophobic |
| O2 | N | ALA- 249 | 3 | 165.58 | H-Bond (Protein Donor) |
| C5M | CD | ARG- 257 | 3.96 | 0 | Hydrophobic |
| N3 | O | HOH- 415 | 2.77 | 144.74 | H-Bond (Ligand Donor) |
| O5' | O | HOH- 434 | 2.67 | 179.97 | H-Bond (Protein Donor) |
