sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.670 Å
X-ray
2011-08-10
| 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 |
|---|---|
| C | 100 % |
| B-Factor: | 36.514 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.335 | 2160.000 |
| % Hydrophobic | % Polar |
|---|---|
| 57.66 | 42.34 |
| According to VolSite | |
| HET Code: | PN0 |
|---|---|
| Formula: | C18H21N3O5S2 |
| Molecular weight: | 423.506 g/mol |
| DrugBank ID: | DB05100 |
| Buried Surface Area: | 67.62 % |
| 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 |
|---|---|---|
| 19.9662 | 29.1257 | 65.134 |
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 | 3.81 | 0 | Hydrophobic |
| S1 | CZ | PHE- 112 | 3.91 | 0 | Hydrophobic |
| C15 | CE1 | PHE- 120 | 3.48 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 121 | 3.76 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 213 | 3.9 | 0 | Hydrophobic |
| C6 | CG | GLU- 216 | 3.99 | 0 | Hydrophobic |
| C3 | CG | GLU- 216 | 4.03 | 0 | Hydrophobic |
| C17 | CB | ALA- 300 | 3.47 | 0 | Hydrophobic |
| C18 | CB | ALA- 300 | 4.29 | 0 | Hydrophobic |
| C17 | CB | ASP- 301 | 3.97 | 0 | Hydrophobic |
| N3 | OG | SER- 304 | 3.12 | 141.58 | H-Bond (Ligand Donor) |
| C10 | CB | SER- 304 | 3.93 | 0 | Hydrophobic |
| C15 | CB | ALA- 305 | 3.67 | 0 | Hydrophobic |
| C12 | CG2 | THR- 309 | 3.85 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 484 | 3.95 | 0 | Hydrophobic |
