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
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 | 73 % |
| B | 27 % |
| B-Factor: | 22.625 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.504 | 459.000 |
| % Hydrophobic | % Polar |
|---|---|
| 44.85 | 55.15 |
| According to VolSite | |
| HET Code: | UTP |
|---|---|
| Formula: | C9H11N2O15P3 |
| Molecular weight: | 480.109 g/mol |
| DrugBank ID: | DB04005 |
| Buried Surface Area: | 60.03 % |
| Polar Surface area: | 299.67 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 15 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 45.613 | -10.1065 | 17.3165 |
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 |
| C2' | CD1 | LEU- 43 | 3.78 | 0 | Hydrophobic |
| O3' | N | GLY- 113 | 3.16 | 163.59 | H-Bond (Protein Donor) |
| O3A | ND1 | HIS- 114 | 3.39 | 131.1 | H-Bond (Protein Donor) |
| O2B | ND1 | HIS- 114 | 3.1 | 155.89 | H-Bond (Protein Donor) |
| O3B | ND1 | HIS- 114 | 2.76 | 129.14 | H-Bond (Protein Donor) |
| O1A | N | GLY- 115 | 3.37 | 120.23 | H-Bond (Protein Donor) |
| O3A | N | GLY- 115 | 3.15 | 168.11 | H-Bond (Protein Donor) |
| C3' | CB | PHE- 116 | 4.45 | 0 | Hydrophobic |
| O1A | N | THR- 117 | 3.04 | 169.71 | H-Bond (Protein Donor) |
| O1A | OG1 | THR- 117 | 2.95 | 157.47 | H-Bond (Protein Donor) |
| C1' | CD | ARG- 217 | 4.08 | 0 | Hydrophobic |
| C4' | CG | ARG- 217 | 4.02 | 0 | Hydrophobic |
| O2B | N | GLY- 218 | 2.86 | 145.87 | H-Bond (Protein Donor) |
| O2 | N | ALA- 249 | 2.95 | 160.36 | H-Bond (Protein Donor) |
| N3 | O | HOH- 402 | 2.79 | 150.03 | H-Bond (Ligand Donor) |
