sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2006-07-04
| Name: | Type 2 DNA topoisomerase 6 subunit B |
|---|---|
| ID: | TOP6B_SULSH |
| AC: | O05207 |
| Organism: | Sulfolobus shibatae |
| Reign: | Archaea |
| TaxID: | 2286 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 19.006 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.597 | 313.875 |
| % Hydrophobic | % Polar |
|---|---|
| 45.16 | 54.84 |
| According to VolSite | |
| HET Code: | RDC |
|---|---|
| Formula: | C18H16ClO6 |
| Molecular weight: | 363.769 g/mol |
| DrugBank ID: | DB03758 |
| Buried Surface Area: | 64.29 % |
| Polar Surface area: | 99.19 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| 16.9422 | -1.26724 | -9.90876 |
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 |
| CL1 | CB | ASN- 42 | 4.45 | 0 | Hydrophobic |
| C5 | CB | ASN- 42 | 3.45 | 0 | Hydrophobic |
| C14 | CB | ASP- 45 | 4.13 | 0 | Hydrophobic |
| C3 | CB | ALA- 46 | 4.11 | 0 | Hydrophobic |
| C16 | CB | ALA- 46 | 3.71 | 0 | Hydrophobic |
| O3 | OD1 | ASP- 76 | 2.54 | 154.94 | H-Bond (Ligand Donor) |
| O3 | OD2 | ASP- 76 | 3.43 | 124.16 | H-Bond (Ligand Donor) |
| C16 | CG1 | ILE- 79 | 3.85 | 0 | Hydrophobic |
| C2 | CG1 | ILE- 81 | 4.06 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 81 | 3.44 | 0 | Hydrophobic |
| C18 | CG1 | ILE- 81 | 4.26 | 0 | Hydrophobic |
| C8 | CZ | PHE- 90 | 4.37 | 0 | Hydrophobic |
| CL1 | CE1 | PHE- 90 | 3.31 | 0 | Hydrophobic |
| CL1 | CG1 | VAL- 112 | 3.7 | 0 | Hydrophobic |
| C2 | CG2 | THR- 170 | 4.17 | 0 | Hydrophobic |
| C3 | CB | THR- 170 | 3.82 | 0 | Hydrophobic |
| C4 | CG2 | THR- 170 | 4.09 | 0 | Hydrophobic |
| O2 | OG1 | THR- 170 | 3.06 | 140.13 | H-Bond (Protein Donor) |
| C5 | CG2 | VAL- 172 | 3.87 | 0 | Hydrophobic |
