sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.850 Å
X-ray
2011-02-03
| Name: | Cytochrome P450 2D6 |
|---|---|
| ID: | CP2D6_HUMAN |
| AC: | P10635 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 64.618 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.501 | 1258.875 |
| % Hydrophobic | % Polar |
|---|---|
| 63.54 | 36.46 |
| According to VolSite | |
| HET Code: | PN0 |
|---|---|
| Formula: | C18H21N3O5S2 |
| Molecular weight: | 423.506 g/mol |
| DrugBank ID: | DB05100 |
| Buried Surface Area: | 70.85 % |
| Polar Surface area: | 142.51 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -9.68493 | -10.4973 | 31.8936 |
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 |
| C4 | CD1 | LEU- 110 | 3.44 | 0 | Hydrophobic |
| S1 | CZ | PHE- 112 | 4.03 | 0 | Hydrophobic |
| C15 | CE1 | PHE- 120 | 3.46 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 213 | 4.06 | 0 | Hydrophobic |
| C6 | CG | GLU- 216 | 4.1 | 0 | Hydrophobic |
| C4 | CB | GLN- 244 | 4.08 | 0 | Hydrophobic |
| C3 | CG | GLN- 244 | 4.33 | 0 | Hydrophobic |
| C18 | CD2 | PHE- 247 | 3.38 | 0 | Hydrophobic |
| S1 | CD2 | LEU- 248 | 4.45 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 248 | 3.96 | 0 | Hydrophobic |
| C17 | CB | ALA- 300 | 3.24 | 0 | Hydrophobic |
| N3 | OG | SER- 304 | 3.46 | 140.11 | H-Bond (Ligand Donor) |
| C17 | CB | SER- 304 | 4.47 | 0 | Hydrophobic |
| C2 | CB | SER- 304 | 4.17 | 0 | Hydrophobic |
| C18 | CB | SER- 304 | 4.36 | 0 | Hydrophobic |
| C15 | CB | ALA- 305 | 3.82 | 0 | Hydrophobic |
| C9 | CG2 | VAL- 308 | 4.09 | 0 | Hydrophobic |
| C12 | CG2 | THR- 309 | 3.97 | 0 | Hydrophobic |
| C7 | CE2 | PHE- 483 | 3.49 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 484 | 4.24 | 0 | Hydrophobic |
