sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
1995-03-30
| Name: | Cytochrome b2, mitochondrial |
|---|---|
| ID: | CYB2_YEAST |
| AC: | P00175 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | 1.1.2.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 28.847 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | FMN |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.993 | 1647.000 |
| % Hydrophobic | % Polar |
|---|---|
| 61.48 | 38.52 |
| According to VolSite | |
| HET Code: | PPY |
|---|---|
| Formula: | C9H7O3 |
| Molecular weight: | 163.150 g/mol |
| DrugBank ID: | DB03884 |
| Buried Surface Area: | 74.58 % |
| Polar Surface area: | 57.2 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 67.5476 | 51.7918 | 6.743 |
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 |
| C2' | CB | ALA- 198 | 3.73 | 0 | Hydrophobic |
| C3' | CD1 | LEU- 199 | 3.85 | 0 | Hydrophobic |
| C2' | CD2 | LEU- 230 | 3.73 | 0 | Hydrophobic |
| O2 | OH | TYR- 254 | 2.99 | 144.78 | H-Bond (Protein Donor) |
| C6' | CD2 | LEU- 286 | 3.73 | 0 | Hydrophobic |
| O1 | NE2 | HIS- 373 | 2.92 | 149.68 | H-Bond (Protein Donor) |
| O2 | NE2 | HIS- 373 | 3.13 | 146.6 | H-Bond (Protein Donor) |
