sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.350 Å
X-ray
2012-09-13
| 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 |
|---|---|
| C | 100 % |
| B-Factor: | 60.104 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.641 | 364.500 |
| % Hydrophobic | % Polar |
|---|---|
| 60.19 | 39.81 |
| According to VolSite | |
| HET Code: | RWX |
|---|---|
| Formula: | C19H20BrClN7O4S |
| Molecular weight: | 557.829 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 53.39 % |
| Polar Surface area: | 169.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 23.9283 | 4.61418 | 26.9939 |
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 | CG1 | VAL- 49 | 3.87 | 0 | Hydrophobic |
| CL3 | CG1 | VAL- 49 | 4 | 0 | Hydrophobic |
| CL3 | CB | ASN- 52 | 3.82 | 0 | Hydrophobic |
| BR3 | CB | ASN- 52 | 3.84 | 0 | Hydrophobic |
| C1 | CB | ALA- 53 | 4.03 | 0 | Hydrophobic |
| C11 | CG | GLU- 56 | 3.94 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 77 | 4.15 | 0 | Hydrophobic |
| N6 | OD2 | ASP- 79 | 2.67 | 157.66 | H-Bond (Ligand Donor) |
| C12 | CB | ARG- 82 | 3.81 | 0 | Hydrophobic |
| S22 | CB | ARG- 82 | 4.05 | 0 | Hydrophobic |
| DuAr | CZ | ARG- 82 | 3.87 | 10.92 | Pi/Cation |
| C11 | CG1 | ILE- 84 | 4.32 | 0 | Hydrophobic |
| C17 | CG1 | ILE- 84 | 4.31 | 0 | Hydrophobic |
| BR3 | CD1 | ILE- 84 | 3.64 | 0 | Hydrophobic |
| C31 | CG | PRO- 85 | 3.92 | 0 | Hydrophobic |
| S22 | CG | PRO- 85 | 3.58 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 99 | 4.25 | 0 | Hydrophobic |
| BR3 | CG1 | VAL- 99 | 4.39 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 123 | 4.29 | 0 | Hydrophobic |
| BR3 | CG1 | VAL- 123 | 4.02 | 0 | Hydrophobic |
| CL3 | CG2 | VAL- 125 | 3.87 | 0 | Hydrophobic |
| BR3 | CG1 | VAL- 125 | 4.34 | 0 | Hydrophobic |
| O24 | NH2 | ARG- 141 | 2.8 | 142.7 | H-Bond (Protein Donor) |
| O24 | CZ | ARG- 141 | 3.55 | 0 | Ionic (Protein Cationic) |
| C1 | CG2 | THR- 169 | 4.07 | 0 | Hydrophobic |
| C1 | CG1 | ILE- 171 | 4.08 | 0 | Hydrophobic |
| CL3 | CG1 | ILE- 171 | 3.75 | 0 | Hydrophobic |
