sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2009-06-23
| Name: | Sulfide-quinone reductase |
|---|---|
| ID: | SQRD_AQUAE |
| AC: | O67931 |
| Organism: | Aquifex aeolicus |
| Reign: | Bacteria |
| TaxID: | 224324 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 78 % |
| D | 22 % |
| B-Factor: | 36.077 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 5 |
| Water Molecules: | 2 |
| Cofactors: | FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.359 | 1998.000 |
| % Hydrophobic | % Polar |
|---|---|
| 74.49 | 25.51 |
| According to VolSite | |
| HET Code: | DCQ |
|---|---|
| Formula: | C19H30O4 |
| Molecular weight: | 322.439 g/mol |
| DrugBank ID: | DB07640 |
| Buried Surface Area: | 56.02 % |
| Polar Surface area: | 52.6 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 28.7855 | 137.344 | 118.56 |
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 |
| C1M | CG | MET- 315 | 4.29 | 0 | Hydrophobic |
| C2 | CB | MET- 315 | 3.81 | 0 | Hydrophobic |
| C5 | CG2 | ILE- 346 | 3.8 | 0 | Hydrophobic |
| C7 | CD1 | ILE- 346 | 3.63 | 0 | Hydrophobic |
| C4M | CD1 | ILE- 348 | 3.79 | 0 | Hydrophobic |
| C3M | CE2 | PHE- 385 | 3.27 | 0 | Hydrophobic |
| C4M | CD2 | PHE- 385 | 3.65 | 0 | Hydrophobic |
| C1M | CE1 | PHE- 385 | 4.2 | 0 | Hydrophobic |
| C7 | CE1 | PHE- 385 | 4.25 | 0 | Hydrophobic |
| C8 | CD1 | PHE- 385 | 3.63 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 385 | 3.97 | 0 | Aromatic Face/Face |
| C10 | CE2 | TYR- 388 | 3.59 | 0 | Hydrophobic |
| C12 | CE2 | TYR- 388 | 4.13 | 0 | Hydrophobic |
| C13 | CZ | TYR- 388 | 4.22 | 0 | Hydrophobic |
| C15 | CD1 | TYR- 388 | 4.44 | 0 | Hydrophobic |
| C16 | CG | TYR- 388 | 3.69 | 0 | Hydrophobic |
| C15 | CE2 | PHE- 402 | 4.01 | 0 | Hydrophobic |
| C12 | CE2 | PHE- 402 | 3.73 | 0 | Hydrophobic |
| C15 | CE2 | PHE- 402 | 4.09 | 0 | Hydrophobic |
| C9 | CG | GLU- 403 | 4.04 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 406 | 4.24 | 0 | Hydrophobic |
| C1M | CD1 | LEU- 407 | 4.37 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 407 | 3.82 | 0 | Hydrophobic |
