sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.980 Å
X-ray
2013-10-02
| Name: | Cytochrome P450 |
|---|---|
| ID: | Q2GB12_NOVAD |
| AC: | Q2GB12 |
| Organism: | Novosphingobium aromaticivorans |
| Reign: | Bacteria |
| TaxID: | 279238 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 15.123 |
|---|---|
| Number of residues: | 18 |
| Including | |
| Standard Amino Acids: | 16 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.635 | 1147.500 |
| % Hydrophobic | % Polar |
|---|---|
| 53.53 | 46.47 |
| According to VolSite | |
| HET Code: | CAM |
|---|---|
| Formula: | C10H16O |
| Molecular weight: | 152.233 g/mol |
| DrugBank ID: | DB01744 |
| Buried Surface Area: | 76.68 % |
| Polar Surface area: | 17.07 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 0 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| 27.9989 | 27.2668 | 2.39555 |
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 |
| C3 | CD1 | ILE- 88 | 4.15 | 0 | Hydrophobic |
| C3 | CZ3 | TRP- 89 | 4.21 | 0 | Hydrophobic |
| C9 | CZ3 | TRP- 89 | 3.86 | 0 | Hydrophobic |
| C10 | CH2 | TRP- 89 | 3.86 | 0 | Hydrophobic |
| O | OH | TYR- 98 | 2.62 | 155.06 | H-Bond (Protein Donor) |
| C3 | CZ | TYR- 98 | 4.4 | 0 | Hydrophobic |
| C3 | CG2 | THR- 103 | 3.7 | 0 | Hydrophobic |
| C10 | CG2 | THR- 187 | 4.08 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 252 | 4.14 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 252 | 3.78 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 255 | 3.8 | 0 | Hydrophobic |
| C8 | CG2 | VAL- 303 | 3.68 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 303 | 3.85 | 0 | Hydrophobic |
| C9 | CB | ASP- 305 | 4.36 | 0 | Hydrophobic |
| C9 | CG2 | ILE- 403 | 4.03 | 0 | Hydrophobic |
| C8 | CG2 | VAL- 404 | 4.38 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 404 | 4.06 | 0 | Hydrophobic |
