sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2013-02-11
| Name: | Cytochrome P450 monooxygenase |
|---|---|
| ID: | Q5YNS8_NOCFA |
| AC: | Q5YNS8 |
| Organism: | Nocardia farcinica |
| Reign: | Bacteria |
| TaxID: | 247156 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 35.913 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.714 | 1134.000 |
| % Hydrophobic | % Polar |
|---|---|
| 63.99 | 36.01 |
| According to VolSite | |
| HET Code: | PLO |
|---|---|
| Formula: | C21H32O2 |
| Molecular weight: | 316.478 g/mol |
| DrugBank ID: | DB02789 |
| Buried Surface Area: | 66.35 % |
| Polar Surface area: | 37.29 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 14.3102 | 35.2966 | 15.5202 |
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 |
| C18 | CE | MET- 84 | 4.11 | 0 | Hydrophobic |
| C19 | CE | MET- 84 | 4.29 | 0 | Hydrophobic |
| C11 | CE | MET- 84 | 3.54 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 87 | 4.07 | 0 | Hydrophobic |
| C7 | CD2 | PHE- 92 | 3.94 | 0 | Hydrophobic |
| C8 | CE2 | PHE- 92 | 4.06 | 0 | Hydrophobic |
| C15 | CE1 | PHE- 92 | 3.95 | 0 | Hydrophobic |
| C18 | CZ | PHE- 92 | 4.12 | 0 | Hydrophobic |
| C19 | CE2 | PHE- 92 | 4.45 | 0 | Hydrophobic |
| C1 | CE2 | PHE- 179 | 3.69 | 0 | Hydrophobic |
| C2 | CZ | PHE- 179 | 3.59 | 0 | Hydrophobic |
| C19 | CZ | PHE- 179 | 4.19 | 0 | Hydrophobic |
| C11 | CZ | PHE- 180 | 4.23 | 0 | Hydrophobic |
| C3 | CB | GLN- 239 | 4.48 | 0 | Hydrophobic |
| C7 | CB | ALA- 240 | 3.77 | 0 | Hydrophobic |
| C9 | CB | ALA- 243 | 4.44 | 0 | Hydrophobic |
| C1 | CB | ALA- 243 | 3.81 | 0 | Hydrophobic |
| C16 | CB | ALA- 244 | 3.85 | 0 | Hydrophobic |
| C17 | CG2 | THR- 248 | 4.47 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 291 | 3.7 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 294 | 3.82 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 294 | 3.87 | 0 | Hydrophobic |
| O20 | NE2 | GLN- 398 | 2.88 | 157.54 | H-Bond (Protein Donor) |
