sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2012-08-01
| 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: | 16.097 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.578 | 239.625 |
| % Hydrophobic | % Polar |
|---|---|
| 52.11 | 47.89 |
| According to VolSite | |
| HET Code: | 0WT |
|---|---|
| Formula: | C17H19ClN7O |
| Molecular weight: | 372.832 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.68 % |
| Polar Surface area: | 107.46 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 |
|---|---|---|
| -10.2403 | -4.85015 | -14.7652 |
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 | 3.74 | 0 | Hydrophobic |
| CL1 | CB | ASN- 48 | 3.53 | 0 | Hydrophobic |
| C3 | CB | ASN- 48 | 3.87 | 0 | Hydrophobic |
| C14 | CB | ASN- 48 | 4.12 | 0 | Hydrophobic |
| C21 | CG | GLU- 52 | 4.42 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 73 | 4.08 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 75 | 2.66 | 167.59 | H-Bond (Ligand Donor) |
| DuAr | CZ | ARG- 78 | 3.82 | 157.27 | Pi/Cation |
| CL1 | CD1 | ILE- 80 | 3.96 | 0 | Hydrophobic |
| C3 | CG1 | ILE- 80 | 3.47 | 0 | Hydrophobic |
| C17 | CG2 | ILE- 80 | 4.03 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 80 | 4.36 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 96 | 3.99 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 96 | 3.84 | 0 | Hydrophobic |
| CL1 | CZ | PHE- 97 | 4.37 | 0 | Hydrophobic |
| N19 | O | GLY- 119 | 3.08 | 162.95 | H-Bond (Ligand Donor) |
| CL1 | CB | SER- 122 | 4.49 | 0 | Hydrophobic |
| C11 | CG2 | THR- 167 | 3.77 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 169 | 3.83 | 0 | Hydrophobic |
| N9 | O | HOH- 407 | 2.83 | 179.97 | H-Bond (Protein Donor) |
