sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.690 Å
X-ray
2012-11-12
| 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: | 18.831 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.374 | 236.250 |
| % Hydrophobic | % Polar |
|---|---|
| 51.43 | 48.57 |
| According to VolSite | |
| HET Code: | 1A0 |
|---|---|
| Formula: | C19H20ClN8S |
| Molecular weight: | 427.934 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.48 % |
| Polar Surface area: | 136.42 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -10.0757 | -5.83359 | -15.408 |
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 |
| C6 | CG2 | ILE- 52 | 3.82 | 0 | Hydrophobic |
| CL1 | CB | ASN- 55 | 3.36 | 0 | Hydrophobic |
| C6 | CB | ASN- 55 | 4.27 | 0 | Hydrophobic |
| C3 | CB | ASN- 55 | 4.16 | 0 | Hydrophobic |
| C17 | CB | ASN- 55 | 4.22 | 0 | Hydrophobic |
| N18 | OD1 | ASN- 55 | 2.84 | 167.17 | H-Bond (Ligand Donor) |
| S19 | CG | GLU- 59 | 3.72 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 80 | 4.25 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 82 | 2.74 | 161.87 | H-Bond (Ligand Donor) |
| S19 | CB | ARG- 85 | 4.4 | 0 | Hydrophobic |
| C21 | CB | ARG- 85 | 3.89 | 0 | Hydrophobic |
| DuAr | CZ | ARG- 85 | 3.73 | 22.62 | Pi/Cation |
| DuAr | CZ | ARG- 85 | 3.7 | 21.54 | Pi/Cation |
| CL1 | CD1 | ILE- 87 | 4.13 | 0 | Hydrophobic |
| C3 | CG1 | ILE- 87 | 3.41 | 0 | Hydrophobic |
| C14 | CG2 | ILE- 87 | 3.84 | 0 | Hydrophobic |
| C21 | CG | PRO- 88 | 4.2 | 0 | Hydrophobic |
| CL1 | CG1 | VAL- 103 | 4.46 | 0 | Hydrophobic |
| C17 | CG1 | VAL- 103 | 3.97 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 103 | 4.1 | 0 | Hydrophobic |
| CL1 | CZ | PHE- 104 | 4.39 | 0 | Hydrophobic |
| CL1 | CB | SER- 129 | 4.39 | 0 | Hydrophobic |
| C7 | CG2 | THR- 174 | 3.85 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 176 | 3.7 | 0 | Hydrophobic |
| N11 | O | HOH- 414 | 2.76 | 144.25 | H-Bond (Protein Donor) |
