sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2007-07-08
| Name: | Cytochrome b |
|---|---|
| ID: | CYB_RHOSH |
| AC: | Q02761 |
| Organism: | Rhodobacter sphaeroides |
| Reign: | Bacteria |
| TaxID: | 1063 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| G | 100 % |
| B-Factor: | 69.500 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.411 | 985.500 |
| % Hydrophobic | % Polar |
|---|---|
| 69.86 | 30.14 |
| According to VolSite | |
| HET Code: | ANJ |
|---|---|
| Formula: | C28H40N2O9 |
| Molecular weight: | 548.625 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 43.62 % |
| Polar Surface area: | 157.32 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 74.6858 | 22.4778 | 35.8531 |
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 |
| C23 | CB | ALA- 29 | 3.58 | 0 | Hydrophobic |
| C4 | CG2 | THR- 37 | 4.02 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 41 | 3.66 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 49 | 4.45 | 0 | Hydrophobic |
| C15 | CB | ALA- 52 | 3.67 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 55 | 4.43 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 209 | 4.44 | 0 | Hydrophobic |
| C27 | CG1 | VAL- 209 | 4.2 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 213 | 3.81 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 213 | 3.89 | 0 | Hydrophobic |
| C6 | CE1 | PHE- 244 | 3.34 | 0 | Hydrophobic |
| C11 | CE2 | PHE- 244 | 3.57 | 0 | Hydrophobic |
| O2 | OD1 | ASP- 252 | 3.29 | 137.96 | H-Bond (Ligand Donor) |
| N1 | OD1 | ASP- 252 | 2.89 | 126.32 | H-Bond (Ligand Donor) |
