sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2015-03-18
| Name: | Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial | Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial | Succinate dehydrogenase cytochrome b560 |
|---|---|---|---|
| ID: | O44074_ASCSU | DHSD_ASCSU | F1LC27_ASCSU |
| AC: | O44074 | P92507 | F1LC27 |
| Organism: | Ascaris suum | ||
| Reign: | Eukaryota | ||
| TaxID: | 6253 | ||
| EC Number: | / | ||
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 33 % |
| C | 41 % |
| D | 26 % |
| B-Factor: | 58.769 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.351 | 293.625 |
| % Hydrophobic | % Polar |
|---|---|
| 52.87 | 47.13 |
| According to VolSite | |
| HET Code: | FD8 |
|---|---|
| Formula: | C20H9F8NO2 |
| Molecular weight: | 447.278 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 44.49 % |
| Polar Surface area: | 38.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -92.2986 | 24.0605 | -62.6021 |
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 |
| C11 | CD2 | LEU- 60 | 3.25 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 60 | 3.27 | 0 | Hydrophobic |
| F4 | CD1 | LEU- 60 | 3.34 | 0 | Hydrophobic |
| C5 | CB | SER- 72 | 3.68 | 0 | Hydrophobic |
| F2 | CD | ARG- 76 | 3.96 | 0 | Hydrophobic |
| C7 | CD | ARG- 76 | 4.48 | 0 | Hydrophobic |
| F2 | CB | ASP- 106 | 4.15 | 0 | Hydrophobic |
| F1 | CE2 | TYR- 107 | 3.33 | 0 | Hydrophobic |
| F7 | CD2 | TYR- 107 | 3.57 | 0 | Hydrophobic |
| F8 | CG | TYR- 107 | 3.3 | 0 | Hydrophobic |
| F2 | CZ | TYR- 107 | 4.1 | 0 | Hydrophobic |
| F3 | CB | PRO- 193 | 3.88 | 0 | Hydrophobic |
| F3 | CB | SER- 194 | 4.44 | 0 | Hydrophobic |
| F1 | CE2 | TRP- 197 | 3.71 | 0 | Hydrophobic |
| O1 | NE1 | TRP- 197 | 3.43 | 136.99 | H-Bond (Protein Donor) |
| F3 | CD1 | ILE- 242 | 3.99 | 0 | Hydrophobic |
| C7 | CD1 | ILE- 242 | 3.88 | 0 | Hydrophobic |
| C6 | CG1 | ILE- 242 | 3.71 | 0 | Hydrophobic |
