sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.550 Å
X-ray
2007-05-03
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 3.660 | 3.660 | 3.660 | 0.000 | 3.660 | 1 |
| 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: | 11.567 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.336 | 590.625 |
| % Hydrophobic | % Polar |
|---|---|
| 42.29 | 57.71 |
| According to VolSite | |
| HET Code: | V15 |
|---|---|
| Formula: | C12H13N3O |
| Molecular weight: | 215.251 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.34 % |
| Polar Surface area: | 67.47 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -1.95806 | 3.15912 | 10.1349 |
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 |
| N6 | OD2 | ASP- 35 | 2.73 | 161.71 | H-Bond (Ligand Donor) |
| N14 | OD1 | ASP- 35 | 2.9 | 162.25 | H-Bond (Ligand Donor) |
| N14 | OD2 | ASP- 35 | 3.32 | 129.12 | H-Bond (Ligand Donor) |
| C15 | CD1 | TYR- 79 | 3.55 | 0 | Hydrophobic |
| C16 | CD2 | TYR- 79 | 3.59 | 0 | Hydrophobic |
| O15 | N | ASP- 81 | 3.28 | 120.45 | H-Bond (Protein Donor) |
| C16 | CZ | PHE- 116 | 3.55 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 122 | 3.82 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 125 | 4.32 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 125 | 3.71 | 0 | Hydrophobic |
| N14 | OD2 | ASP- 219 | 2.81 | 150.06 | H-Bond (Ligand Donor) |
