sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2015-05-01
| Name: | Cytosol aminopeptidase |
|---|---|
| ID: | AMPA_HELPY |
| AC: | O25294 |
| Organism: | Helicobacter pylori |
| Reign: | Bacteria |
| TaxID: | 85962 |
| EC Number: | 3.4.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 3 % |
| F | 97 % |
| B-Factor: | 10.591 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN ZN NA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.616 | 874.125 |
| % Hydrophobic | % Polar |
|---|---|
| 36.29 | 63.71 |
| According to VolSite | |
| HET Code: | BES |
|---|---|
| Formula: | C16H24N2O4 |
| Molecular weight: | 308.373 g/mol |
| DrugBank ID: | DB03424 |
| Buried Surface Area: | 58.87 % |
| Polar Surface area: | 117.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 13.3975 | 8.18668 | -9.96232 |
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 | NZ | LYS- 270 | 2.82 | 154.9 | H-Bond (Protein Donor) |
| C1 | SD | MET- 278 | 4.48 | 0 | Hydrophobic |
| C10 | CE | MET- 278 | 3.93 | 0 | Hydrophobic |
| C15 | CB | ASP- 340 | 4.15 | 0 | Hydrophobic |
| C13 | CB | ALA- 341 | 4.21 | 0 | Hydrophobic |
| C16 | CB | ALA- 341 | 4.17 | 0 | Hydrophobic |
| N2 | O | THR- 367 | 3.2 | 171.77 | H-Bond (Ligand Donor) |
| C12 | CB | THR- 367 | 3.94 | 0 | Hydrophobic |
| N1 | O | LEU- 368 | 3.23 | 144.56 | H-Bond (Ligand Donor) |
| O4 | N | GLY- 370 | 2.73 | 152.83 | H-Bond (Protein Donor) |
| C9 | CG2 | VAL- 373 | 4.45 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 428 | 3.75 | 0 | Hydrophobic |
| C11 | CB | ALA- 461 | 3.89 | 0 | Hydrophobic |
| O2 | ZN | ZN- 501 | 2 | 0 | Metal Acceptor |
| O2 | ZN | ZN- 502 | 2.31 | 0 | Metal Acceptor |
| O3 | ZN | ZN- 502 | 2.62 | 0 | Metal Acceptor |
