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
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: | 35.317 |
|---|---|
| Number of residues: | 20 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.691 | 378.000 |
| % Hydrophobic | % Polar |
|---|---|
| 71.43 | 28.57 |
| According to VolSite | |
| HET Code: | NBB |
|---|---|
| Formula: | C10H15NO2S |
| Molecular weight: | 213.297 g/mol |
| DrugBank ID: | DB02055 |
| Buried Surface Area: | 58.3 % |
| 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 |
|---|---|---|
| 15.5954 | 13.9542 | -0.931571 |
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 | 3.44 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 53 | 4.34 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 53 | 4.16 | 0 | Hydrophobic |
| C5 | CE2 | PHE- 56 | 3.18 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 58 | 4.32 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 73 | 4.14 | 0 | Hydrophobic |
| C11 | CZ2 | TRP- 116 | 4.01 | 0 | Hydrophobic |
| C12 | CE2 | TRP- 116 | 3.26 | 0 | Hydrophobic |
| C13 | CH2 | TRP- 116 | 4.26 | 0 | Hydrophobic |
| C14 | CE3 | TRP- 116 | 3.85 | 0 | Hydrophobic |
| N10 | O | PHE- 117 | 2.88 | 154.48 | H-Bond (Ligand Donor) |
| C11 | CG2 | VAL- 118 | 4.24 | 0 | Hydrophobic |
| O1S | N | ILE- 119 | 3.05 | 172.74 | H-Bond (Protein Donor) |
| C4 | CD1 | ILE- 119 | 4.49 | 0 | Hydrophobic |
| C3 | CG1 | ILE- 119 | 4.4 | 0 | Hydrophobic |
