sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.150 Å
X-ray
2011-10-20
| Name: | Cytochrome P450 3A4 |
|---|---|
| ID: | CP3A4_HUMAN |
| AC: | P08684 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 39.138 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.770 | 1738.125 |
| % Hydrophobic | % Polar |
|---|---|
| 55.92 | 44.08 |
| According to VolSite | |
| HET Code: | 08Y |
|---|---|
| Formula: | C32H41BrN5O5 |
| Molecular weight: | 655.602 g/mol |
| DrugBank ID: | DB01200 |
| Buried Surface Area: | 66.1 % |
| Polar Surface area: | 119.41 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 7 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 22.7544 | 14.8129 | -11.868 |
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 |
| BR | CE1 | TYR- 53 | 3.71 | 0 | Hydrophobic |
| C23 | CZ | PHE- 57 | 3.57 | 0 | Hydrophobic |
| BR | CE2 | PHE- 57 | 3.67 | 0 | Hydrophobic |
| BR | CB | ASP- 76 | 4.25 | 0 | Hydrophobic |
| C14 | CD | ARG- 105 | 3.88 | 0 | Hydrophobic |
| C30 | CG | ARG- 106 | 3.68 | 0 | Hydrophobic |
| C28 | CD | ARG- 106 | 3.69 | 0 | Hydrophobic |
| C32 | CB | PHE- 108 | 4.48 | 0 | Hydrophobic |
| C20 | CE2 | PHE- 108 | 4.46 | 0 | Hydrophobic |
| C19 | CE2 | PHE- 108 | 3.91 | 0 | Hydrophobic |
| C20 | CB | SER- 119 | 4.26 | 0 | Hydrophobic |
| O4 | OG | SER- 119 | 3.32 | 139.06 | H-Bond (Protein Donor) |
| C20 | CG1 | ILE- 120 | 3.43 | 0 | Hydrophobic |
| C4 | CD | ARG- 212 | 4.45 | 0 | Hydrophobic |
| C19 | CD1 | PHE- 213 | 4.41 | 0 | Hydrophobic |
| C26 | CB | PHE- 215 | 4.38 | 0 | Hydrophobic |
| C23 | CB | PHE- 215 | 4.23 | 0 | Hydrophobic |
| C19 | CZ | PHE- 215 | 4.28 | 0 | Hydrophobic |
| N5 | OG1 | THR- 224 | 3.08 | 143.7 | H-Bond (Ligand Donor) |
| BR | CG2 | THR- 224 | 4.49 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 301 | 4.02 | 0 | Hydrophobic |
| C19 | CZ | PHE- 304 | 4.31 | 0 | Hydrophobic |
| C10 | CE2 | PHE- 304 | 3.29 | 0 | Hydrophobic |
| C7 | CB | ALA- 305 | 4.27 | 0 | Hydrophobic |
| C7 | CG2 | THR- 309 | 3.91 | 0 | Hydrophobic |
| C13 | CB | ALA- 370 | 3.31 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 373 | 4.33 | 0 | Hydrophobic |
