sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2009-12-01
| Name: | Cathepsin S |
|---|---|
| ID: | CATS_HUMAN |
| AC: | P25774 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.22.27 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 17.718 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.741 | 479.250 |
| % Hydrophobic | % Polar |
|---|---|
| 46.48 | 53.52 |
| According to VolSite | |
| HET Code: | 23Z |
|---|---|
| Formula: | C32H41F3N5O4S |
| Molecular weight: | 648.759 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 41.9 % |
| Polar Surface area: | 130.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| 5.732 | -1.07138 | 12.4821 |
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 |
| F41 | CB | TRP- 26 | 3.67 | 0 | Hydrophobic |
| C36 | CG | LYS- 64 | 3.84 | 0 | Hydrophobic |
| C13 | CE2 | PHE- 70 | 3.88 | 0 | Hydrophobic |
| C20 | CE1 | PHE- 70 | 3.84 | 0 | Hydrophobic |
| C30 | CE2 | PHE- 70 | 4.36 | 0 | Hydrophobic |
| C35 | CE1 | PHE- 70 | 3.58 | 0 | Hydrophobic |
| C25 | CE | MET- 71 | 3.97 | 0 | Hydrophobic |
| C38 | SD | MET- 71 | 3.88 | 0 | Hydrophobic |
| C20 | CG2 | THR- 73 | 4.08 | 0 | Hydrophobic |
| O2 | N | VAL- 162 | 3.18 | 156.73 | H-Bond (Protein Donor) |
| C23 | CG2 | VAL- 162 | 3.86 | 0 | Hydrophobic |
| C5 | CZ | PHE- 211 | 3.6 | 0 | Hydrophobic |
| C12 | CE1 | PHE- 211 | 3.79 | 0 | Hydrophobic |
| C24 | CB | PHE- 211 | 3.83 | 0 | Hydrophobic |
| C43 | CE2 | PHE- 211 | 3.7 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 211 | 3.76 | 0 | Aromatic Face/Face |
