sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2004-03-27
| Name: | Acylamino-acid-releasing enzyme |
|---|---|
| ID: | APEH_AERPE |
| AC: | Q9YBQ2 |
| Organism: | Aeropyrum pernix |
| Reign: | Archaea |
| TaxID: | 272557 |
| EC Number: | 3.4.19.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 27.718 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.906 | 442.125 |
| % Hydrophobic | % Polar |
|---|---|
| 58.78 | 41.22 |
| According to VolSite | |
| HET Code: | 4NP |
|---|---|
| Formula: | C6H4NO6P |
| Molecular weight: | 217.073 g/mol |
| DrugBank ID: | DB04214 |
| Buried Surface Area: | 66.74 % |
| Polar Surface area: | 128.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 3 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 49.6408 | 90.2097 | 34.6234 |
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 |
| O3 | N | GLY- 369 | 3.39 | 136.24 | H-Bond (Protein Donor) |
| O1 | OG | SER- 445 | 3.02 | 155.9 | H-Bond (Protein Donor) |
| C5 | SD | MET- 477 | 4.1 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 492 | 4.28 | 0 | Hydrophobic |
| C6 | CG2 | THR- 527 | 3.6 | 0 | Hydrophobic |
