sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.350 Å
X-ray
2012-02-20
| Name: | APH(2'')-Id |
|---|---|
| ID: | O68183_ENTCA |
| AC: | O68183 |
| Organism: | Enterococcus casseliflavus |
| Reign: | Bacteria |
| TaxID: | 37734 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 36.058 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.738 | 735.750 |
| % Hydrophobic | % Polar |
|---|---|
| 40.37 | 59.63 |
| According to VolSite | |
| HET Code: | ADN |
|---|---|
| Formula: | C10H13N5O4 |
| Molecular weight: | 267.241 g/mol |
| DrugBank ID: | DB00640 |
| Buried Surface Area: | 46.78 % |
| Polar Surface area: | 139.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 11.8444 | -44.4676 | 6.86195 |
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 | O | THR- 96 | 3.08 | 129.69 | H-Bond (Ligand Donor) |
| N1 | N | ILE- 98 | 2.75 | 169.3 | H-Bond (Protein Donor) |
| C5' | CD1 | ILE- 216 | 3.82 | 0 | Hydrophobic |
| C2' | CD1 | ILE- 216 | 3.7 | 0 | Hydrophobic |
| O5' | OD2 | ASP- 217 | 3.16 | 146.5 | H-Bond (Ligand Donor) |
