sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.140 Å
X-ray
2013-03-13
| Name: | Cytochrome P450 2B4 |
|---|---|
| ID: | CP2B4_RABIT |
| AC: | P00178 |
| Organism: | Oryctolagus cuniculus |
| Reign: | Eukaryota |
| TaxID: | 9986 |
| EC Number: | 1.14.14.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 35.122 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.357 | 644.625 |
| % Hydrophobic | % Polar |
|---|---|
| 56.54 | 43.46 |
| According to VolSite | |
| HET Code: | 8PR |
|---|---|
| Formula: | C19H21FNO3 |
| Molecular weight: | 330.373 g/mol |
| DrugBank ID: | DB00715 |
| Buried Surface Area: | 70.19 % |
| Polar Surface area: | 44.3 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -32.8439 | -3.59858 | 19.5378 |
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 |
| CAL | CD1 | LEU- 51 | 4.46 | 0 | Hydrophobic |
| CAU | CG1 | ILE- 101 | 4.25 | 0 | Hydrophobic |
| CAF | CD1 | ILE- 101 | 3.92 | 0 | Hydrophobic |
| CAH | CD1 | ILE- 101 | 3.53 | 0 | Hydrophobic |
| FAA | CG2 | ILE- 114 | 3.52 | 0 | Hydrophobic |
| CAJ | CE1 | PHE- 206 | 4.22 | 0 | Hydrophobic |
| CAH | CG2 | ILE- 209 | 4.32 | 0 | Hydrophobic |
| CAL | CG | GLU- 218 | 3.96 | 0 | Hydrophobic |
| CAX | CE2 | PHE- 297 | 4.2 | 0 | Hydrophobic |
| CAB | CB | ALA- 298 | 3.73 | 0 | Hydrophobic |
| NAN | OE1 | GLU- 301 | 3.34 | 134.71 | H-Bond (Ligand Donor) |
| NAN | OE1 | GLU- 301 | 3.34 | 0 | Ionic (Ligand Cationic) |
| CAE | CD1 | ILE- 363 | 4.39 | 0 | Hydrophobic |
| CAM | CG2 | ILE- 363 | 4.05 | 0 | Hydrophobic |
| CAW | CG1 | ILE- 363 | 4.2 | 0 | Hydrophobic |
| CAL | CE1 | PHE- 365 | 4.27 | 0 | Hydrophobic |
| CAM | CG2 | VAL- 367 | 4.42 | 0 | Hydrophobic |
| CAR | CG2 | VAL- 367 | 3.48 | 0 | Hydrophobic |
| CAU | CG | PRO- 368 | 4.49 | 0 | Hydrophobic |
| CAM | CG2 | VAL- 477 | 4.36 | 0 | Hydrophobic |
| CAH | CG2 | VAL- 477 | 3.58 | 0 | Hydrophobic |
