sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.640 Å
X-ray
2011-05-18
| Name: | Cathepsin B-like peptidase (C01 family) |
|---|---|
| ID: | Q8MNY2_SCHMA |
| AC: | Q8MNY2 |
| Organism: | Schistosoma mansoni |
| Reign: | Eukaryota |
| TaxID: | 6183 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 17 % |
| B | 83 % |
| B-Factor: | 56.001 |
|---|---|
| Number of residues: | 45 |
| Including | |
| Standard Amino Acids: | 45 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.053 | 1674.000 |
| % Hydrophobic | % Polar |
|---|---|
| 44.76 | 55.24 |
| According to VolSite | |
| HET Code: | 0IW |
|---|---|
| Formula: | C32H41N4O4S |
| Molecular weight: | 577.757 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.52 % |
| Polar Surface area: | 108.39 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 3.05446 | -5.55361 | 13.9367 |
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 |
| CM | CD | ARG- 79 | 4.2 | 0 | Hydrophobic |
| C5 | CG | LYS- 80 | 4.27 | 0 | Hydrophobic |
| C5' | CB | LYS- 80 | 4.22 | 0 | Hydrophobic |
| C3' | CD | LYS- 80 | 4.15 | 0 | Hydrophobic |
| CD2 | CB | PRO- 83 | 4.2 | 0 | Hydrophobic |
| CE1 | CG | PRO- 83 | 4.35 | 0 | Hydrophobic |
| O11 | NE2 | GLN- 94 | 3.26 | 131.38 | H-Bond (Protein Donor) |
| CM | CD1 | LEU- 139 | 3.82 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 139 | 3.75 | 0 | Hydrophobic |
| N | O | GLY- 144 | 3.12 | 141.86 | H-Bond (Ligand Donor) |
| O1 | N | GLY- 144 | 3.2 | 168.51 | H-Bond (Protein Donor) |
| C3 | CG1 | ILE- 145 | 4.32 | 0 | Hydrophobic |
| CD2 | CD1 | LEU- 146 | 3.76 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 193 | 4.11 | 0 | Hydrophobic |
| N2 | O | GLY- 269 | 3.01 | 147.81 | H-Bond (Ligand Donor) |
| C11 | CB | HIS- 270 | 3.97 | 0 | Hydrophobic |
| CB | CB | ALA- 271 | 4.31 | 0 | Hydrophobic |
