sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2011-07-24
| Name: | Sulfide-quinone reductase |
|---|---|
| ID: | SQRD_ACIF2 |
| AC: | B7JBP8 |
| Organism: | Acidithiobacillus ferrooxidans ) |
| Reign: | Bacteria |
| TaxID: | 243159 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 43.715 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.996 | 681.750 |
| % Hydrophobic | % Polar |
|---|---|
| 65.84 | 34.16 |
| According to VolSite | |
| HET Code: | DCQ |
|---|---|
| Formula: | C19H30O4 |
| Molecular weight: | 322.439 g/mol |
| DrugBank ID: | DB07640 |
| Buried Surface Area: | 58.06 % |
| 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 |
|---|---|---|
| 43.1392 | -8.0683 | 5.85978 |
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 |
| C3M | CZ | PHE- 41 | 3.23 | 0 | Hydrophobic |
| C3M | CG | PRO- 43 | 3.55 | 0 | Hydrophobic |
| C13 | CD1 | TYR- 323 | 4 | 0 | Hydrophobic |
| C16 | CD2 | TYR- 323 | 3.72 | 0 | Hydrophobic |
| C16 | CB | ASN- 353 | 3.78 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 355 | 4.35 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 355 | 4.21 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 355 | 4.23 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 355 | 4.23 | 0 | Hydrophobic |
| C2 | CB | PHE- 357 | 4.2 | 0 | Hydrophobic |
| C1M | CZ | PHE- 357 | 3.32 | 0 | Hydrophobic |
| C7 | CE2 | PHE- 357 | 3.98 | 0 | Hydrophobic |
| C1 | CE2 | PHE- 357 | 3.41 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 368 | 4.31 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 368 | 3.83 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 368 | 4.24 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 370 | 4.49 | 0 | Hydrophobic |
| C3M | CD2 | PHE- 394 | 3.31 | 0 | Hydrophobic |
| C4M | CE2 | PHE- 394 | 3.69 | 0 | Hydrophobic |
| C8 | CE1 | PHE- 394 | 4.31 | 0 | Hydrophobic |
| C1M | CB | PHE- 394 | 3.97 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 394 | 3.93 | 0 | Aromatic Face/Face |
| O5 | OH | TYR- 411 | 3.42 | 143.54 | H-Bond (Protein Donor) |
| C9 | CD2 | TYR- 411 | 4.2 | 0 | Hydrophobic |
| C8 | CE2 | TYR- 411 | 3.9 | 0 | Hydrophobic |
