sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.120 Å
X-ray
2015-02-10
| Name: | Endothiapepsin |
|---|---|
| ID: | CARP_CRYPA |
| AC: | P11838 |
| Organism: | Cryphonectria parasitica |
| Reign: | Eukaryota |
| TaxID: | 5116 |
| EC Number: | 3.4.23.22 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 12.953 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.923 | 742.500 |
| % Hydrophobic | % Polar |
|---|---|
| 45.45 | 54.55 |
| According to VolSite | |
| HET Code: | F41 |
|---|---|
| Formula: | C14H19N2O3 |
| Molecular weight: | 263.312 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 50.58 % |
| Polar Surface area: | 52 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -1.05568 | 6.79868 | 8.99153 |
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 |
| C6 | CG | TYR- 79 | 3.41 | 0 | Hydrophobic |
| N4 | OD2 | ASP- 81 | 2.86 | 139.94 | H-Bond (Ligand Donor) |
| N4 | OD2 | ASP- 81 | 2.86 | 0 | Ionic (Ligand Cationic) |
| O9 | N | ASP- 81 | 2.98 | 135.03 | H-Bond (Protein Donor) |
| C1 | CZ | PHE- 116 | 3.99 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 125 | 3.98 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 217 | 4.18 | 0 | Hydrophobic |
| N10 | OG1 | THR- 222 | 2.81 | 155.48 | H-Bond (Ligand Donor) |
| C18 | CB | ILE- 300 | 4.47 | 0 | Hydrophobic |
| C14 | CG2 | ILE- 300 | 3.85 | 0 | Hydrophobic |
| C14 | CG2 | ILE- 302 | 4.32 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 304 | 3.24 | 0 | Hydrophobic |
