sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2010-07-14
| 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: | 31.230 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.303 | 2376.000 |
| % Hydrophobic | % Polar |
|---|---|
| 52.70 | 47.30 |
| According to VolSite | |
| HET Code: | RIT |
|---|---|
| Formula: | C37H48N6O5S2 |
| Molecular weight: | 720.944 g/mol |
| DrugBank ID: | DB00503 |
| Buried Surface Area: | 68.88 % |
| Polar Surface area: | 202.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 18 |
| X | Y | Z |
|---|---|---|
| 36.6859 | -15.6936 | 29.6905 |
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 |
| C86 | CE1 | TYR- 53 | 4.25 | 0 | Hydrophobic |
| C75 | CZ | PHE- 57 | 4.07 | 0 | Hydrophobic |
| C44 | CD | ARG- 105 | 4.04 | 0 | Hydrophobic |
| C90 | CD | ARG- 106 | 4.2 | 0 | Hydrophobic |
| C13 | CE2 | PHE- 108 | 3.96 | 0 | Hydrophobic |
| C26 | CZ | PHE- 108 | 3.59 | 0 | Hydrophobic |
| C62 | CD2 | PHE- 108 | 4.35 | 0 | Hydrophobic |
| C68 | CE2 | PHE- 108 | 3.83 | 0 | Hydrophobic |
| C90 | CB | PHE- 108 | 4.5 | 0 | Hydrophobic |
| C35 | CE | MET- 114 | 4.06 | 0 | Hydrophobic |
| N11 | OG | SER- 119 | 2.83 | 157.02 | H-Bond (Ligand Donor) |
| O41 | OG | SER- 119 | 3.15 | 162.76 | H-Bond (Ligand Donor) |
| C13 | CB | SER- 119 | 4.5 | 0 | Hydrophobic |
| C26 | CD1 | ILE- 120 | 4.19 | 0 | Hydrophobic |
| C33 | CD2 | LEU- 210 | 3.54 | 0 | Hydrophobic |
| C31 | CD1 | LEU- 211 | 3.66 | 0 | Hydrophobic |
| C68 | CD1 | LEU- 211 | 4.27 | 0 | Hydrophobic |
| C32 | CB | LEU- 211 | 3.72 | 0 | Hydrophobic |
| C64 | CD1 | PHE- 213 | 3.87 | 0 | Hydrophobic |
| C90 | CZ | PHE- 213 | 4.27 | 0 | Hydrophobic |
| C86 | CZ | PHE- 215 | 3.48 | 0 | Hydrophobic |
| C86 | CG2 | THR- 224 | 3.87 | 0 | Hydrophobic |
| C26 | CZ | PHE- 241 | 4.32 | 0 | Hydrophobic |
| C34 | CG2 | ILE- 300 | 4.36 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 301 | 4.48 | 0 | Hydrophobic |
| C35 | CD1 | ILE- 301 | 3.57 | 0 | Hydrophobic |
| C6 | CD2 | PHE- 304 | 3.78 | 0 | Hydrophobic |
| C33 | CG | PHE- 304 | 3.37 | 0 | Hydrophobic |
| C6 | CB | ALA- 305 | 3.86 | 0 | Hydrophobic |
| S3 | CG2 | THR- 309 | 4.22 | 0 | Hydrophobic |
| S3 | CD1 | ILE- 369 | 4.35 | 0 | Hydrophobic |
| C51 | CD1 | ILE- 369 | 3.36 | 0 | Hydrophobic |
| C50 | CB | ALA- 370 | 3.55 | 0 | Hydrophobic |
| C75 | CB | ARG- 372 | 4.49 | 0 | Hydrophobic |
| C95 | CB | ARG- 372 | 3.5 | 0 | Hydrophobic |
| C49 | CD2 | LEU- 373 | 4.4 | 0 | Hydrophobic |
| C95 | CG | GLU- 374 | 3.83 | 0 | Hydrophobic |
