sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2012-11-13
| Name: | DNA gyrase subunit B |
|---|---|
| ID: | GYRB_ECOLI |
| AC: | P0AES6 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 3 % |
| D | 97 % |
| B-Factor: | 30.253 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.038 | 1252.125 |
| % Hydrophobic | % Polar |
|---|---|
| 40.43 | 59.57 |
| According to VolSite | |
| HET Code: | 1A1 |
|---|---|
| Formula: | C17H13N7OS |
| Molecular weight: | 363.396 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.12 % |
| Polar Surface area: | 126.71 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -23.1287 | -3.20392 | 28.1724 |
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 |
| C11 | CG1 | VAL- 43 | 3.38 | 0 | Hydrophobic |
| C10 | CB | ALA- 47 | 3.69 | 0 | Hydrophobic |
| S15 | CG | GLU- 50 | 4.45 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 71 | 3.99 | 0 | Hydrophobic |
| N7 | OD1 | ASP- 73 | 2.74 | 169.79 | H-Bond (Ligand Donor) |
| S15 | CB | ARG- 76 | 4.15 | 0 | Hydrophobic |
| DuAr | CZ | ARG- 76 | 3.84 | 157.78 | Pi/Cation |
| S15 | CG1 | ILE- 78 | 4.42 | 0 | Hydrophobic |
| C17 | CG | PRO- 79 | 4.39 | 0 | Hydrophobic |
| C17 | CB | PHE- 104 | 3.86 | 0 | Hydrophobic |
| C12 | CG2 | THR- 169 | 3.59 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 171 | 3.85 | 0 | Hydrophobic |
| N24 | O | HOH- 402 | 2.68 | 179.95 | H-Bond (Protein Donor) |
| N1 | O | HOH- 407 | 2.92 | 179.95 | H-Bond (Protein Donor) |
| O9 | O | HOH- 441 | 2.93 | 172.45 | H-Bond (Protein Donor) |
