sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2001-05-25
| Name: | Glucose-1-phosphate thymidylyltransferase 1 |
|---|---|
| ID: | RMLA1_ECOLI |
| AC: | P37744 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 29.266 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.891 | 1022.625 |
| % Hydrophobic | % Polar |
|---|---|
| 36.96 | 63.04 |
| According to VolSite | |
| HET Code: | TMP |
|---|---|
| Formula: | C10H13N2O8P |
| Molecular weight: | 320.193 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 49.19 % |
| Polar Surface area: | 161.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 30.0785 | -24.0266 | 61.7934 |
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 |
| O2 | N | GLY- 11 | 2.9 | 123.31 | H-Bond (Protein Donor) |
| N3 | OE1 | GLN- 83 | 2.57 | 169.06 | H-Bond (Ligand Donor) |
| C5M | CB | PRO- 86 | 4.42 | 0 | Hydrophobic |
| O4 | N | GLY- 88 | 2.58 | 155.06 | H-Bond (Protein Donor) |
| C5' | CD2 | LEU- 89 | 4.34 | 0 | Hydrophobic |
| C5M | CD2 | LEU- 89 | 4.33 | 0 | Hydrophobic |
| C4' | CD1 | LEU- 109 | 4.39 | 0 | Hydrophobic |
