sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.760 Å
X-ray
2013-10-23
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.330 | 6.330 | 6.330 | 0.000 | 6.330 | 1 |
| Name: | Caspase-6 |
|---|---|
| ID: | CASP6_HUMAN |
| AC: | P55212 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.22.59 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 30 % |
| B | 70 % |
| B-Factor: | 15.324 |
|---|---|
| Number of residues: | 20 |
| Including | |
| Standard Amino Acids: | 19 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.773 | 394.875 |
| % Hydrophobic | % Polar |
|---|---|
| 63.25 | 36.75 |
| According to VolSite | |
| HET Code: | 2J6 |
|---|---|
| Formula: | C16H13FN4O |
| Molecular weight: | 296.299 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.43 % |
| Polar Surface area: | 70.93 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 30.021 | 23.7161 | -5.49677 |
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 |
| F16 | CB | ALA- 195 | 3.35 | 0 | Hydrophobic |
| C8 | CD1 | TYR- 198 | 4.11 | 0 | Hydrophobic |
| C14 | CB | TYR- 198 | 4.48 | 0 | Hydrophobic |
| C2 | CB | TYR- 198 | 3.58 | 0 | Hydrophobic |
| C2 | CB | TYR- 198 | 3.71 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 198 | 3.68 | 0 | Aromatic Face/Face |
| DuAr | DuAr | TYR- 198 | 3.61 | 0 | Aromatic Face/Face |
| O15 | N | THR- 199 | 3.1 | 160.61 | H-Bond (Protein Donor) |
| C3 | CD2 | LEU- 200 | 4.18 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 200 | 3.51 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 200 | 3.98 | 0 | Hydrophobic |
| C14 | CG | PRO- 201 | 4.27 | 0 | Hydrophobic |
| C10 | CG | GLU- 214 | 3.48 | 0 | Hydrophobic |
| C9 | CB | GLU- 214 | 3.49 | 0 | Hydrophobic |
| C13 | CB | GLU- 214 | 3.49 | 0 | Hydrophobic |
