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
2012-08-09
| Name: | DNA gyrase subunit B |
|---|---|
| ID: | GYRB_MYCSM |
| AC: | P0C559 |
| Organism: | Mycobacterium smegmatis |
| Reign: | Bacteria |
| TaxID: | 1772 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 86 % |
| B | 14 % |
| B-Factor: | 39.580 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.552 | 600.750 |
| % Hydrophobic | % Polar |
|---|---|
| 47.19 | 52.81 |
| According to VolSite | |
| HET Code: | B5U |
|---|---|
| Formula: | C27H35N6O2 |
| Molecular weight: | 475.606 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.79 % |
| Polar Surface area: | 97.81 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 21.9222 | 29.3392 | 76.6162 |
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 |
| C1 | CG2 | VAL- 49 | 4.44 | 0 | Hydrophobic |
| C5 | CB | ASN- 52 | 3.71 | 0 | Hydrophobic |
| N17 | OD2 | ASP- 79 | 2.98 | 170.09 | H-Bond (Ligand Donor) |
| C23 | CD | ARG- 82 | 4.07 | 0 | Hydrophobic |
| C24 | CB | ARG- 82 | 4.25 | 0 | Hydrophobic |
| DuAr | CZ | ARG- 82 | 3.87 | 33.47 | Pi/Cation |
| C4 | CD1 | ILE- 84 | 3.92 | 0 | Hydrophobic |
| C26 | CG | PRO- 85 | 4.17 | 0 | Hydrophobic |
| C22 | CG | PRO- 85 | 3.5 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 99 | 3.95 | 0 | Hydrophobic |
| C8 | CB | GLN- 102 | 4.47 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 123 | 3.83 | 0 | Hydrophobic |
| C1 | CB | SER- 126 | 3.75 | 0 | Hydrophobic |
| C8 | CB | SER- 126 | 3.9 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 128 | 3.89 | 0 | Hydrophobic |
| C3 | CG1 | ILE- 171 | 4.06 | 0 | Hydrophobic |
| C27 | CG | GLN- 195 | 4.43 | 0 | Hydrophobic |
| O16 | O | HOH- 2020 | 2.69 | 158.03 | H-Bond (Protein Donor) |
| O25 | O | HOH- 2030 | 2.97 | 179.94 | H-Bond (Protein Donor) |
