sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2008-05-26
| Name: | Cellular tumor antigen p53 |
|---|---|
| ID: | P53_HUMAN |
| AC: | P04637 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 15.060 |
|---|---|
| Number of residues: | 20 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.795 | 249.750 |
| % Hydrophobic | % Polar |
|---|---|
| 52.70 | 47.30 |
| According to VolSite | |
| HET Code: | P83 |
|---|---|
| Formula: | C16H19N2 |
| Molecular weight: | 239.335 g/mol |
| DrugBank ID: | DB08363 |
| Buried Surface Area: | 58.4 % |
| Polar Surface area: | 21.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 0 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 124.684 | 105.073 | -43.1216 |
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 |
| C92 | CB | LEU- 145 | 3.65 | 0 | Hydrophobic |
| C92 | CG1 | VAL- 147 | 3.79 | 0 | Hydrophobic |
| C4A | CG2 | VAL- 147 | 3.37 | 0 | Hydrophobic |
| C9A | CG2 | VAL- 147 | 3.33 | 0 | Hydrophobic |
| C6 | CG2 | THR- 150 | 3.34 | 0 | Hydrophobic |
| C8 | CG | PRO- 151 | 3.87 | 0 | Hydrophobic |
| C8 | SG | CYS- 220 | 4.3 | 0 | Hydrophobic |
| C92 | SG | CYS- 220 | 3.4 | 0 | Hydrophobic |
| C5 | CB | PRO- 222 | 4.02 | 0 | Hydrophobic |
| C6 | CG | PRO- 222 | 3.46 | 0 | Hydrophobic |
| C4A | CG | PRO- 223 | 3.82 | 0 | Hydrophobic |
| C4A | CG | PRO- 223 | 3.82 | 0 | Hydrophobic |
| N32 | O | ASP- 228 | 2.74 | 160.65 | H-Bond (Ligand Donor) |
| C91 | CB | THR- 230 | 3.7 | 0 | Hydrophobic |
