sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.200 Å
X-ray
2015-04-20
| 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: | 12.295 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.744 | 739.125 |
| % Hydrophobic | % Polar |
|---|---|
| 39.27 | 60.73 |
| According to VolSite | |
| HET Code: | IMI |
|---|---|
| Formula: | C10H17N3O2S |
| Molecular weight: | 243.326 g/mol |
| DrugBank ID: | DB03353 |
| Buried Surface Area: | 56.45 % |
| Polar Surface area: | 115.08 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -3.96919 | 1.88963 | 10.4502 |
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 |
| O12 | OD2 | ASP- 35 | 2.52 | 161.83 | H-Bond (Ligand Donor) |
| O12 | OD1 | ASP- 35 | 3.13 | 130.04 | H-Bond (Ligand Donor) |
| C10 | CD1 | TYR- 79 | 3.7 | 0 | Hydrophobic |
| C9 | CG | TYR- 79 | 3.95 | 0 | Hydrophobic |
| N2 | OD2 | ASP- 81 | 2.63 | 172.85 | H-Bond (Ligand Donor) |
| C4 | CB | SER- 115 | 4.24 | 0 | Hydrophobic |
| C7 | CZ | PHE- 116 | 4.27 | 0 | Hydrophobic |
| C6 | CE1 | PHE- 116 | 3.71 | 0 | Hydrophobic |
| C2 | CE1 | PHE- 116 | 3.32 | 0 | Hydrophobic |
| C6 | CB | ASP- 119 | 4.44 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 122 | 3.81 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 125 | 4.01 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 125 | 4.23 | 0 | Hydrophobic |
