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
2011-07-20
| 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: | 47.697 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.121 | 540.000 |
| % Hydrophobic | % Polar |
|---|---|
| 68.13 | 31.88 |
| According to VolSite | |
| HET Code: | DCQ |
|---|---|
| Formula: | C19H30O4 |
| Molecular weight: | 322.439 g/mol |
| DrugBank ID: | DB07640 |
| Buried Surface Area: | 56.11 % |
| 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 |
|---|---|---|
| 42.5811 | -9.62513 | 5.91217 |
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 | CG2 | THR- 11 | 3.85 | 0 | Hydrophobic |
| C4M | CZ | PHE- 41 | 3.53 | 0 | Hydrophobic |
| C3M | CG | PRO- 43 | 3.43 | 0 | Hydrophobic |
| C4M | CG | PRO- 43 | 3.87 | 0 | Hydrophobic |
| C4 | CG | PRO- 43 | 4.37 | 0 | Hydrophobic |
| C1M | CB | TYR- 323 | 3.82 | 0 | Hydrophobic |
| C12 | CB | TYR- 323 | 4.43 | 0 | Hydrophobic |
| C14 | CG | TYR- 323 | 4.15 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 355 | 3.96 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 355 | 3.64 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 355 | 4.16 | 0 | Hydrophobic |
| C8 | CE2 | PHE- 357 | 3.65 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 368 | 4.45 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 368 | 3.96 | 0 | Hydrophobic |
| C4M | CD | LYS- 391 | 3.96 | 0 | Hydrophobic |
| C4M | CD2 | PHE- 394 | 3.48 | 0 | Hydrophobic |
| C1M | CZ | PHE- 394 | 3.9 | 0 | Hydrophobic |
| C9 | CD1 | PHE- 394 | 4.14 | 0 | Hydrophobic |
| C3 | CE2 | PHE- 394 | 3.3 | 0 | Hydrophobic |
| O2 | OH | TYR- 411 | 3.01 | 129.78 | H-Bond (Ligand Donor) |
| C1M | CZ | TYR- 411 | 3.36 | 0 | Hydrophobic |
| O5 | N3 | FAD- 500 | 3.46 | 152.72 | H-Bond (Protein Donor) |
