sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2005-03-17
| 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 | 95 % |
| B | 5 % |
| B-Factor: | 22.358 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.733 | 499.500 |
| % Hydrophobic | % Polar |
|---|---|
| 54.73 | 45.27 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.6 % |
| Polar Surface area: | 260.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 33.8183 | 19.9146 | 136.062 |
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 |
| C4' | CE1 | PHE- 7 | 4.45 | 0 | Hydrophobic |
| C1' | CE1 | PHE- 7 | 4.37 | 0 | Hydrophobic |
| O2A | ND2 | ASN- 42 | 2.97 | 151.91 | H-Bond (Protein Donor) |
| N6 | OD1 | ASP- 76 | 3 | 163.75 | H-Bond (Ligand Donor) |
| C4' | CB | ALA- 89 | 4.14 | 0 | Hydrophobic |
| C1' | CB | ALA- 89 | 4.25 | 0 | Hydrophobic |
| O3B | OG | SER- 96 | 2.69 | 167.72 | H-Bond (Protein Donor) |
| O3' | N | SER- 97 | 3.11 | 172.46 | H-Bond (Protein Donor) |
| O2' | OG | SER- 97 | 2.63 | 148.11 | H-Bond (Ligand Donor) |
| O1B | NZ | LYS- 98 | 2.96 | 170.78 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 98 | 2.96 | 0 | Ionic (Protein Cationic) |
| O3B | NZ | LYS- 98 | 3.98 | 0 | Ionic (Protein Cationic) |
| O2B | N | GLY- 109 | 2.92 | 153.5 | H-Bond (Protein Donor) |
| O1A | N | VAL- 112 | 3.31 | 138.04 | H-Bond (Protein Donor) |
| O2A | N | VAL- 112 | 3.36 | 160.44 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 113 | 2.55 | 137.49 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 113 | 2.55 | 0 | Ionic (Protein Cationic) |
| O1B | MG | MG- 2001 | 2.09 | 0 | Metal Acceptor |
| O2A | MG | MG- 2001 | 2.13 | 0 | Metal Acceptor |
| N1 | O | HOH- 3003 | 2.74 | 179.95 | H-Bond (Protein Donor) |
