sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2008-06-10
| Name: | Caspase-3 |
|---|---|
| ID: | CASP3_HUMAN |
| AC: | P42574 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.22.56 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 58 % |
| C | 42 % |
| B-Factor: | 55.144 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.408 | 1225.125 |
| % Hydrophobic | % Polar |
|---|---|
| 43.53 | 56.47 |
| According to VolSite | |
| HET Code: | RXB |
|---|---|
| Formula: | C19H13N2O6 |
| Molecular weight: | 365.316 g/mol |
| DrugBank ID: | DB08497 |
| Buried Surface Area: | 51.33 % |
| Polar Surface area: | 120.71 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -46.798 | 15.02 | -21.9013 |
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 |
| CAN | CG2 | THR- 166 | 3.88 | 0 | Hydrophobic |
| CAK | CG2 | THR- 166 | 4.36 | 0 | Hydrophobic |
| CAM | CB | THR- 166 | 3.33 | 0 | Hydrophobic |
| CAM | CD1 | LEU- 168 | 3.46 | 0 | Hydrophobic |
| CBA | CD1 | LEU- 168 | 4.43 | 0 | Hydrophobic |
| CAA | CB | LEU- 168 | 4.02 | 0 | Hydrophobic |
| OAB | N | LEU- 168 | 2.84 | 162.07 | H-Bond (Protein Donor) |
| CAJ | CB | TYR- 204 | 4.2 | 0 | Hydrophobic |
| CAN | CG2 | THR- 255 | 4.43 | 0 | Hydrophobic |
| CAG | CG2 | THR- 255 | 3.58 | 0 | Hydrophobic |
| CAK | CG2 | THR- 255 | 3.92 | 0 | Hydrophobic |
