sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2012-08-03
| Name: | DNA gyrase subunit B |
|---|---|
| ID: | GYRB_ENTFA |
| AC: | Q839Z1 |
| Organism: | Enterococcus faecalis |
| Reign: | Bacteria |
| TaxID: | 226185 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 21.190 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.269 | 270.000 |
| % Hydrophobic | % Polar |
|---|---|
| 50.00 | 50.00 |
| According to VolSite | |
| HET Code: | SUY |
|---|---|
| Formula: | C17H19ClN7S |
| Molecular weight: | 388.898 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.43 % |
| Polar Surface area: | 123.52 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -10.1032 | -4.91369 | -14.835 |
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 |
| C10 | CG2 | ILE- 45 | 3.7 | 0 | Hydrophobic |
| CL1 | CB | ASN- 48 | 3.44 | 0 | Hydrophobic |
| C10 | CB | ASN- 48 | 4.48 | 0 | Hydrophobic |
| C5 | CB | ASN- 48 | 3.94 | 0 | Hydrophobic |
| C14 | CB | ASN- 48 | 4.08 | 0 | Hydrophobic |
| S20 | CG | GLU- 52 | 3.79 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 73 | 4.17 | 0 | Hydrophobic |
| N7 | OD1 | ASP- 75 | 2.63 | 164.58 | H-Bond (Ligand Donor) |
| DuAr | CZ | ARG- 78 | 3.74 | 161.18 | Pi/Cation |
| CL1 | CD1 | ILE- 80 | 3.99 | 0 | Hydrophobic |
| C5 | CG1 | ILE- 80 | 3.41 | 0 | Hydrophobic |
| C17 | CG2 | ILE- 80 | 4 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 80 | 4.4 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 96 | 4 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 96 | 4 | 0 | Hydrophobic |
| N19 | O | GLY- 119 | 3.1 | 163.16 | H-Bond (Ligand Donor) |
| C11 | CG2 | THR- 167 | 3.76 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 169 | 3.81 | 0 | Hydrophobic |
| N1 | O | HOH- 426 | 2.73 | 179.98 | H-Bond (Protein Donor) |
