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: | 59.245 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.369 | 536.625 |
| % Hydrophobic | % Polar |
|---|---|
| 76.73 | 23.27 |
| According to VolSite | |
| HET Code: | ET |
|---|---|
| Formula: | C21H20N3 |
| Molecular weight: | 314.404 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.35 % |
| Polar Surface area: | 55.92 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -14.3735 | 22.3404 | -3.42671 |
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 |
| C22 | CD2 | PHE- 67 | 3.37 | 0 | Hydrophobic |
| C12 | CE1 | PHE- 67 | 3.46 | 0 | Hydrophobic |
| C4 | CB | PHE- 67 | 4.28 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 67 | 3.84 | 0 | Aromatic Face/Face |
| C2 | CG2 | VAL- 70 | 3.99 | 0 | Hydrophobic |
| N24 | O | LEU- 88 | 3.41 | 158.39 | H-Bond (Ligand Donor) |
| C10 | CG1 | VAL- 91 | 4.1 | 0 | Hydrophobic |
| C9 | CB | LEU- 92 | 3.72 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 92 | 4.19 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 92 | 3.6 | 0 | Hydrophobic |
| C10 | CB | TRP- 95 | 4.5 | 0 | Hydrophobic |
| C1 | CB | TRP- 95 | 3.63 | 0 | Hydrophobic |
| DuAr | DuAr | TRP- 95 | 3.71 | 0 | Aromatic Face/Face |
| N23 | OE2 | GLU- 106 | 2.9 | 132.3 | H-Bond (Ligand Donor) |
| N23 | OE1 | GLU- 106 | 3.27 | 147.35 | H-Bond (Ligand Donor) |
| C22 | CE2 | TRP- 126 | 3.65 | 0 | Hydrophobic |
| C17 | CB | ALA- 127 | 3.68 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 147 | 3.83 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 150 | 3.66 | 0 | Hydrophobic |
| C19 | CB | LEU- 150 | 3.31 | 0 | Hydrophobic |
| C20 | SG | CYS- 154 | 4.17 | 0 | Hydrophobic |
