sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.860 Å
X-ray
2012-08-11
| Name: | Aminoglycoside 3'-phosphotransferase AphA1-IAB |
|---|---|
| ID: | B0VD92_ACIBY |
| AC: | B0VD92 |
| Organism: | Acinetobacter baumannii |
| Reign: | Bacteria |
| TaxID: | 509173 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| I | 93 % |
| J | 7 % |
| B-Factor: | 49.102 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.984 | 1535.625 |
| % Hydrophobic | % Polar |
|---|---|
| 31.21 | 68.79 |
| According to VolSite | |
| HET Code: | 0J9 |
|---|---|
| Formula: | C19H19N5 |
| Molecular weight: | 317.388 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.21 % |
| Polar Surface area: | 69.62 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 79.6948 | 40.5762 | 12.1736 |
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 |
| CAE | CG | GLN- 5 | 4.41 | 0 | Hydrophobic |
| CAF | CB | ASP- 31 | 4.3 | 0 | Hydrophobic |
| CAF | CG2 | VAL- 33 | 4.48 | 0 | Hydrophobic |
| CAA | CG2 | ILE- 40 | 4.17 | 0 | Hydrophobic |
| CAB | CD1 | ILE- 40 | 3.62 | 0 | Hydrophobic |
| CAA | CG | PHE- 53 | 3.63 | 0 | Hydrophobic |
| C5 | CE2 | PHE- 53 | 3.4 | 0 | Hydrophobic |
| N1 | N | ILE- 101 | 3 | 166.72 | H-Bond (Protein Donor) |
| NAD | O | ILE- 101 | 2.96 | 165.54 | H-Bond (Ligand Donor) |
| CAG | CG2 | THR- 105 | 4.06 | 0 | Hydrophobic |
| CAI | CD1 | ILE- 205 | 4.03 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 215 | 3.94 | 0 | Hydrophobic |
| CAC | CB | ILE- 215 | 4.05 | 0 | Hydrophobic |
| CAQ | CD1 | ILE- 215 | 4.37 | 0 | Hydrophobic |
