sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.890 Å
X-ray
2012-05-30
| 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 |
|---|---|
| A | 96 % |
| B | 4 % |
| B-Factor: | 24.705 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.412 | 688.500 |
| % Hydrophobic | % Polar |
|---|---|
| 38.24 | 61.76 |
| According to VolSite | |
| HET Code: | PP1 |
|---|---|
| Formula: | C16H19N5 |
| Molecular weight: | 281.356 g/mol |
| DrugBank ID: | DB01809 |
| Buried Surface Area: | 60.44 % |
| Polar Surface area: | 69.62 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -21.3573 | -28.5553 | -19.0528 |
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 |
| C15 | CG | GLN- 5 | 4.06 | 0 | Hydrophobic |
| C24 | CG | GLN- 5 | 4.37 | 0 | Hydrophobic |
| C29 | CD1 | ILE- 40 | 3.63 | 0 | Hydrophobic |
| C37 | CG2 | ILE- 40 | 4.28 | 0 | Hydrophobic |
| C37 | CB | PHE- 53 | 3.53 | 0 | Hydrophobic |
| C5 | CE2 | PHE- 53 | 3.4 | 0 | Hydrophobic |
| N7 | N | ILE- 101 | 2.99 | 166.92 | H-Bond (Protein Donor) |
| N10 | O | ILE- 101 | 2.93 | 159.8 | H-Bond (Ligand Donor) |
| C14 | CG2 | THR- 105 | 4.3 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 205 | 4.2 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 215 | 3.83 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 215 | 4.23 | 0 | Hydrophobic |
| C28 | CD1 | ILE- 215 | 4.45 | 0 | Hydrophobic |
| C33 | CB | ILE- 215 | 3.91 | 0 | Hydrophobic |
