sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2005-05-15
| Name: | Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial | Succinate dehydrogenase cytochrome b560 subunit, mitochondrial |
|---|---|---|
| ID: | SDHB_PIG | C560_PIG |
| AC: | Q007T0 | D0VWV4 |
| Organism: | Sus scrofa | |
| Reign: | Eukaryota | |
| TaxID: | 9823 | |
| EC Number: | 1.3.5.1 | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 32 % |
| C | 58 % |
| D | 11 % |
| B-Factor: | 64.496 |
|---|---|
| Number of residues: | 20 |
| Including | |
| Standard Amino Acids: | 19 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.224 | 320.625 |
| % Hydrophobic | % Polar |
|---|---|
| 64.21 | 35.79 |
| According to VolSite | |
| HET Code: | UQ1 |
|---|---|
| Formula: | C14H18O4 |
| Molecular weight: | 250.290 g/mol |
| DrugBank ID: | DB08689 |
| Buried Surface Area: | 56.87 % |
| 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: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 86.1445 | 65.7146 | 85.3924 |
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 |
| C10 | CB | ILE- 30 | 3.28 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 30 | 3.36 | 0 | Hydrophobic |
| CM5 | CZ3 | TRP- 35 | 3.64 | 0 | Hydrophobic |
| C8 | CH2 | TRP- 35 | 4.37 | 0 | Hydrophobic |
| C10 | CH2 | TRP- 35 | 3.86 | 0 | Hydrophobic |
| CM5 | CG | MET- 39 | 4.16 | 0 | Hydrophobic |
| CM3 | CB | SER- 42 | 4.5 | 0 | Hydrophobic |
| CM5 | CD1 | ILE- 43 | 3.38 | 0 | Hydrophobic |
| CM3 | CD | ARG- 46 | 3.84 | 0 | Hydrophobic |
| O1 | OH | TYR- 91 | 3.27 | 121.71 | H-Bond (Protein Donor) |
| O2 | OH | TYR- 91 | 2.63 | 160.1 | H-Bond (Protein Donor) |
| CM2 | CE2 | TYR- 91 | 4 | 0 | Hydrophobic |
| CM2 | CB | PRO- 169 | 3.95 | 0 | Hydrophobic |
| O1 | NE1 | TRP- 173 | 2.8 | 140.68 | H-Bond (Protein Donor) |
| C7 | CZ2 | TRP- 173 | 4.27 | 0 | Hydrophobic |
| C11 | CZ2 | TRP- 173 | 3.89 | 0 | Hydrophobic |
| CM3 | CD1 | ILE- 218 | 4.29 | 0 | Hydrophobic |
