sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2007-11-12
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.810 | 6.810 | 6.810 | 0.000 | 6.810 | 1 |
| Name: | Cathepsin L1 |
|---|---|
| ID: | CATL1_HUMAN |
| AC: | P07711 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.22.15 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 80 % |
| B | 20 % |
| B-Factor: | 23.676 |
|---|---|
| Number of residues: | 58 |
| Including | |
| Standard Amino Acids: | 53 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.771 | 1809.000 |
| % Hydrophobic | % Polar |
|---|---|
| 42.35 | 57.65 |
| According to VolSite | |
| HET Code: | OPT |
|---|---|
| Formula: | C47H56N7O5S |
| Molecular weight: | 831.056 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 49.18 % |
| Polar Surface area: | 230.58 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 8 |
| Rings: | 5 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 23 |
| X | Y | Z |
|---|---|---|
| -15.6161 | 4.78963 | 7.45918 |
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 |
| C54 | CD | ARG- 8 | 4.31 | 0 | Hydrophobic |
| C52 | CB | ARG- 8 | 3.76 | 0 | Hydrophobic |
| C56 | CG | GLU- 9 | 3.96 | 0 | Hydrophobic |
| C6 | CG | GLN- 19 | 3.97 | 0 | Hydrophobic |
| N29 | OD2 | CSD- 25 | 3.35 | 138.25 | H-Bond (Ligand Donor) |
| C55 | CG | GLU- 63 | 3.61 | 0 | Hydrophobic |
| O39 | N | GLY- 68 | 2.93 | 148.55 | H-Bond (Protein Donor) |
| N60 | O | GLY- 68 | 3.19 | 165.59 | H-Bond (Ligand Donor) |
| C53 | CG | LEU- 69 | 3.96 | 0 | Hydrophobic |
| C50 | CD2 | LEU- 69 | 3.54 | 0 | Hydrophobic |
| C46 | SD | MET- 70 | 3.49 | 0 | Hydrophobic |
| C49 | CB | ALA- 135 | 3.43 | 0 | Hydrophobic |
| C22 | CB | ALA- 138 | 4.32 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 144 | 4.4 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 144 | 3.64 | 0 | Hydrophobic |
| N29 | O | ASP- 162 | 3.11 | 131.13 | H-Bond (Ligand Donor) |
| N40 | O | ASP- 162 | 2.97 | 168.09 | H-Bond (Ligand Donor) |
| C32 | CB | ASP- 162 | 4.13 | 0 | Hydrophobic |
| SG2 | CB | HIS- 163 | 4.1 | 0 | Hydrophobic |
| C11 | CB | TRP- 189 | 4.05 | 0 | Hydrophobic |
| C11 | CE3 | TRP- 189 | 3.47 | 0 | Hydrophobic |
| SG2 | CZ2 | TRP- 189 | 3.89 | 0 | Hydrophobic |
| O3 | NE1 | TRP- 189 | 3.02 | 153.93 | H-Bond (Protein Donor) |
| C50 | CB | ALA- 214 | 3.82 | 0 | Hydrophobic |
