sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2008-05-20
| Name: | Pheromone-binding protein ASP1 |
|---|---|
| ID: | Q9U9J6_APIME |
| AC: | Q9U9J6 |
| Organism: | Apis mellifera |
| Reign: | Eukaryota |
| TaxID: | 7460 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 33.827 |
|---|---|
| Number of residues: | 19 |
| Including | |
| Standard Amino Acids: | 19 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.930 | 465.750 |
| % Hydrophobic | % Polar |
|---|---|
| 82.61 | 17.39 |
| According to VolSite | |
| HET Code: | NBB |
|---|---|
| Formula: | C10H15NO2S |
| Molecular weight: | 213.297 g/mol |
| DrugBank ID: | DB02055 |
| Buried Surface Area: | 63.36 % |
| Polar Surface area: | 54.55 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 15.8931 | 14.0791 | -0.414857 |
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 |
| C2 | CH2 | TRP- 4 | 3.42 | 0 | Hydrophobic |
| C2 | CG2 | VAL- 5 | 4.16 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 53 | 4.4 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 53 | 3.83 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 58 | 3.74 | 0 | Hydrophobic |
| C12 | CE | MET- 70 | 4.48 | 0 | Hydrophobic |
| C14 | SD | MET- 70 | 4.45 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 73 | 4.12 | 0 | Hydrophobic |
| C1 | CB | LEU- 73 | 4.18 | 0 | Hydrophobic |
| C11 | CZ2 | TRP- 116 | 3.78 | 0 | Hydrophobic |
| C12 | CH2 | TRP- 116 | 4.03 | 0 | Hydrophobic |
| C13 | CE3 | TRP- 116 | 4.03 | 0 | Hydrophobic |
| O1S | N | ILE- 119 | 3.01 | 172.21 | H-Bond (Protein Donor) |
| C3 | CD1 | ILE- 119 | 3.94 | 0 | Hydrophobic |
