sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2009-06-11
| Name: | EbrA repressor |
|---|---|
| ID: | Q79SH7_STRLI |
| AC: | Q79SH7 |
| Organism: | Streptomyces lividans |
| Reign: | Bacteria |
| TaxID: | 1916 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 67.208 |
|---|---|
| Number of residues: | 17 |
| Including | |
| Standard Amino Acids: | 17 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.513 | 435.375 |
| % Hydrophobic | % Polar |
|---|---|
| 79.07 | 20.93 |
| According to VolSite | |
| HET Code: | PRL |
|---|---|
| Formula: | C13H11N3 |
| Molecular weight: | 209.247 g/mol |
| DrugBank ID: | DB01123 |
| Buried Surface Area: | 64.92 % |
| Polar Surface area: | 64.92 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| -40.9408 | 26.1667 | 9.85344 |
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 |
| C4 | CB | PHE- 67 | 4.24 | 0 | Hydrophobic |
| C1 | CE1 | PHE- 67 | 3.48 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 70 | 4.24 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 70 | 4.13 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 91 | 4.3 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 92 | 4.38 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 92 | 3.83 | 0 | Hydrophobic |
| C13 | CE3 | TRP- 95 | 3.48 | 0 | Hydrophobic |
| C12 | CZ3 | TRP- 95 | 3.49 | 0 | Hydrophobic |
| C2 | CB | TRP- 95 | 3.55 | 0 | Hydrophobic |
| DuAr | DuAr | TRP- 95 | 3.47 | 0 | Aromatic Face/Face |
| C12 | CZ2 | TRP- 126 | 3.46 | 0 | Hydrophobic |
| C5 | CZ2 | TRP- 126 | 3.39 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 150 | 3.95 | 0 | Hydrophobic |
| C8 | SG | CYS- 154 | 4.12 | 0 | Hydrophobic |
