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
2007-07-09
| 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 |
|---|---|
| A | 85 % |
| F | 15 % |
| B-Factor: | 46.100 |
|---|---|
| Number of residues: | 47 |
| Including | |
| Standard Amino Acids: | 46 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.850 | 985.500 |
| % Hydrophobic | % Polar |
|---|---|
| 73.97 | 26.03 |
| According to VolSite | |
| HET Code: | SMA |
|---|---|
| Formula: | C30H42O7 |
| Molecular weight: | 514.650 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.64 % |
| Polar Surface area: | 83.45 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 88.8492 | 91.1229 | 148.773 |
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 |
| C25 | CD2 | LEU- 137 | 3.56 | 0 | Hydrophobic |
| C22 | SD | MET- 140 | 4.25 | 0 | Hydrophobic |
| C23 | CE | MET- 140 | 4.05 | 0 | Hydrophobic |
| C25 | CE | MET- 140 | 3.96 | 0 | Hydrophobic |
| C24 | CB | PHE- 144 | 3.71 | 0 | Hydrophobic |
| C26 | CE2 | PHE- 144 | 3.91 | 0 | Hydrophobic |
| C21 | SD | MET- 145 | 4 | 0 | Hydrophobic |
| C5M | CB | CYS- 151 | 3.85 | 0 | Hydrophobic |
| O4 | NE2 | HIS- 152 | 2.84 | 170.94 | H-Bond (Protein Donor) |
| C7M | SD | MET- 154 | 4.19 | 0 | Hydrophobic |
| C5M | CG2 | VAL- 161 | 4.32 | 0 | Hydrophobic |
| C6 | CB | VAL- 161 | 4.48 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 161 | 3.63 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 162 | 4.07 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 162 | 4.03 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 162 | 4.4 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 162 | 3.97 | 0 | Hydrophobic |
| C26 | CE1 | PHE- 166 | 4.21 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 180 | 4.04 | 0 | Hydrophobic |
| C26 | CD1 | LEU- 180 | 4.02 | 0 | Hydrophobic |
| C21 | CE1 | PHE- 194 | 3.88 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 197 | 3.88 | 0 | Hydrophobic |
| C5M | CG1 | ILE- 292 | 4.39 | 0 | Hydrophobic |
| C7M | CG1 | ILE- 292 | 3.63 | 0 | Hydrophobic |
| C8 | CB | PRO- 294 | 3.61 | 0 | Hydrophobic |
| C7 | CG | PRO- 294 | 3.74 | 0 | Hydrophobic |
| O8 | OE1 | GLU- 295 | 2.6 | 130.39 | H-Bond (Ligand Donor) |
| C9 | CB | PHE- 298 | 4.19 | 0 | Hydrophobic |
| C24 | CZ | PHE- 298 | 3.82 | 0 | Hydrophobic |
| C22 | CD1 | PHE- 298 | 3.76 | 0 | Hydrophobic |
| C22 | CB | PHE- 301 | 3.91 | 0 | Hydrophobic |
| C3M | CD1 | TYR- 302 | 4.2 | 0 | Hydrophobic |
| C5M | CE1 | TYR- 302 | 3.77 | 0 | Hydrophobic |
| C3M | CD1 | LEU- 305 | 4.31 | 0 | Hydrophobic |
| C3M | SD | MET- 336 | 3.49 | 0 | Hydrophobic |
| C22 | SD | MET- 336 | 4.4 | 0 | Hydrophobic |
| C23 | CE | MET- 336 | 3.83 | 0 | Hydrophobic |
| C9 | SD | MET- 336 | 4.28 | 0 | Hydrophobic |
| C14 | CZ | PHE- 337 | 4.41 | 0 | Hydrophobic |
| C23 | CE1 | PHE- 337 | 3.55 | 0 | Hydrophobic |
| C23 | CD1 | ILE- 340 | 3.55 | 0 | Hydrophobic |
