sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
1999-08-31
| Name: | DNA topoisomerase 1 |
|---|---|
| ID: | TOP1_ECOLI |
| AC: | P06612 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 30.010 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.076 | 766.125 |
| % Hydrophobic | % Polar |
|---|---|
| 34.36 | 65.64 |
| According to VolSite | |
| HET Code: | TMP |
|---|---|
| Formula: | C10H13N2O8P |
| Molecular weight: | 320.193 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 54.73 % |
| 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 |
|---|---|---|
| 40.4153 | 20.4505 | 42.2464 |
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 |
| C3' | CD1 | LEU- 112 | 4.5 | 0 | Hydrophobic |
| C1' | CB | ASP- 113 | 4 | 0 | Hydrophobic |
| C5M | CB | ASP- 113 | 4.2 | 0 | Hydrophobic |
| O2P | NH2 | ARG- 114 | 3.43 | 173.05 | H-Bond (Protein Donor) |
| O3P | NE | ARG- 114 | 2.88 | 176.4 | H-Bond (Protein Donor) |
| O3P | CZ | ARG- 114 | 3.72 | 0 | Ionic (Protein Cationic) |
| C5M | CB | ARG- 114 | 3.92 | 0 | Hydrophobic |
| C5M | CB | GLU- 115 | 3.52 | 0 | Hydrophobic |
| O1P | CZ | ARG- 161 | 3.81 | 0 | Ionic (Protein Cationic) |
| O3P | CZ | ARG- 161 | 3.44 | 0 | Ionic (Protein Cationic) |
| O1P | NE | ARG- 161 | 2.98 | 123.57 | H-Bond (Protein Donor) |
| O3P | NH2 | ARG- 161 | 3.19 | 136.41 | H-Bond (Protein Donor) |
| O3P | NE | ARG- 161 | 2.82 | 160.07 | H-Bond (Protein Donor) |
| O4' | NH2 | ARG- 161 | 2.95 | 126.16 | H-Bond (Protein Donor) |
| O4 | NH2 | ARG- 168 | 2.96 | 131.08 | H-Bond (Protein Donor) |
| O4 | NE | ARG- 168 | 2.8 | 137.67 | H-Bond (Protein Donor) |
| C5M | CB | SER- 495 | 3.61 | 0 | Hydrophobic |
