sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2006-06-27
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.500 | 7.500 | 7.500 | 0.000 | 7.500 | 1 |
| 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 | 20 % |
| B | 80 % |
| B-Factor: | 23.947 |
|---|---|
| Number of residues: | 48 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | CL ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.235 | 509.625 |
| % Hydrophobic | % Polar |
|---|---|
| 60.26 | 39.74 |
| According to VolSite | |
| HET Code: | GNQ |
|---|---|
| Formula: | C25H31F3N4O6S |
| Molecular weight: | 572.597 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.27 % |
| Polar Surface area: | 134.44 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 15.0964 | -2.01405 | -8.9451 |
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 |
| C16 | SG | CYS- 25 | 4.29 | 0 | Hydrophobic |
| C8 | SG | CYS- 25 | 4.1 | 0 | Hydrophobic |
| C16 | CB | TRP- 26 | 4.38 | 0 | Hydrophobic |
| C14 | CD | LYS- 64 | 4.13 | 0 | Hydrophobic |
| O2 | NZ | LYS- 64 | 2.95 | 150.93 | H-Bond (Protein Donor) |
| N | O | GLY- 69 | 2.86 | 144.12 | H-Bond (Ligand Donor) |
| O | N | GLY- 69 | 3.25 | 144.82 | H-Bond (Protein Donor) |
| C17 | CD1 | PHE- 70 | 3.79 | 0 | Hydrophobic |
| C13 | CE2 | PHE- 70 | 3.47 | 0 | Hydrophobic |
| C19 | CE | MET- 71 | 3.95 | 0 | Hydrophobic |
| F3 | CB | ALA- 140 | 4.39 | 0 | Hydrophobic |
| C5 | CB | ALA- 140 | 3.92 | 0 | Hydrophobic |
| C5 | CB | ARG- 141 | 4.22 | 0 | Hydrophobic |
| C8 | CB | PRO- 143 | 3.98 | 0 | Hydrophobic |
| C4 | CB | PRO- 143 | 3.9 | 0 | Hydrophobic |
| C6 | CG | PRO- 143 | 3.9 | 0 | Hydrophobic |
| F1 | CB | PHE- 146 | 3.33 | 0 | Hydrophobic |
| F2 | CB | PHE- 146 | 4.21 | 0 | Hydrophobic |
| F3 | CB | PHE- 146 | 4.29 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 147 | 4.28 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 147 | 4.28 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 162 | 3.64 | 0 | Hydrophobic |
| N2 | O | ASN- 163 | 2.95 | 139.99 | H-Bond (Ligand Donor) |
| C6 | CB | ASN- 163 | 3.98 | 0 | Hydrophobic |
| C6 | CB | HIS- 164 | 3.64 | 0 | Hydrophobic |
| F3 | CH2 | TRP- 186 | 3.79 | 0 | Hydrophobic |
| C22 | CB | PHE- 211 | 3.6 | 0 | Hydrophobic |
