sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.600 Å
X-ray
2012-05-03
| Name: | Possible succinate dehydrogenase |
|---|---|
| ID: | Q0S4Q9_RHOJR |
| AC: | Q0S4Q9 |
| Organism: | Rhodococcus jostii |
| Reign: | Bacteria |
| TaxID: | 101510 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 12.450 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.177 | 421.875 |
| % Hydrophobic | % Polar |
|---|---|
| 64.00 | 36.00 |
| According to VolSite | |
| HET Code: | ASD |
|---|---|
| Formula: | C19H26O2 |
| Molecular weight: | 286.409 g/mol |
| DrugBank ID: | DB01536 |
| Buried Surface Area: | 68.2 % |
| Polar Surface area: | 34.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| 33.4777 | 17.2022 | 40.7952 |
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 |
| C6 | CE2 | PHE- 66 | 4.18 | 0 | Hydrophobic |
| C15 | CB | TRP- 136 | 3.92 | 0 | Hydrophobic |
| C18 | CE2 | TRP- 136 | 3.46 | 0 | Hydrophobic |
| C19 | CZ3 | TRP- 136 | 3.45 | 0 | Hydrophobic |
| C7 | CB | TRP- 136 | 4.26 | 0 | Hydrophobic |
| C8 | CE3 | TRP- 136 | 4.04 | 0 | Hydrophobic |
| C2 | CG | GLU- 290 | 4.29 | 0 | Hydrophobic |
| C18 | CB | ALA- 292 | 4.08 | 0 | Hydrophobic |
| C11 | CB | ALA- 292 | 3.62 | 0 | Hydrophobic |
| C15 | CG2 | THR- 354 | 3.78 | 0 | Hydrophobic |
| C16 | CE1 | PHE- 356 | 4.1 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 357 | 4.05 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 357 | 4.37 | 0 | Hydrophobic |
| C2 | CE2 | PHE- 427 | 3.84 | 0 | Hydrophobic |
| C2 | CE2 | TYR- 466 | 3.68 | 0 | Hydrophobic |
| O1 | OH | TYR- 466 | 2.7 | 170.72 | H-Bond (Protein Donor) |
| O1 | OG | SER- 468 | 3.46 | 124.82 | H-Bond (Protein Donor) |
| O1 | N | GLY- 469 | 3.39 | 148.95 | H-Bond (Protein Donor) |
| C2 | C9A | FAD- 1492 | 3.8 | 0 | Hydrophobic |
| C7 | C6 | FAD- 1492 | 4.48 | 0 | Hydrophobic |
| C12 | C7M | FAD- 1492 | 4.15 | 0 | Hydrophobic |
| C1 | C6 | FAD- 1492 | 3.66 | 0 | Hydrophobic |
