sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2012-11-26
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.350 | 7.350 | 7.350 | 0.000 | 7.350 | 2 |
| Name: | Acetylcholine-binding protein |
|---|---|
| ID: | ACHP_LYMST |
| AC: | P58154 |
| Organism: | Lymnaea stagnalis |
| Reign: | Eukaryota |
| TaxID: | 6523 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| F | 57 % |
| G | 43 % |
| B-Factor: | 15.143 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.989 | 475.875 |
| % Hydrophobic | % Polar |
|---|---|
| 53.19 | 46.81 |
| According to VolSite | |
| HET Code: | XRS |
|---|---|
| Formula: | C10H20N3O |
| Molecular weight: | 198.285 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 83.39 % |
| Polar Surface area: | 31.49 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 60.5234 | -9.67393 | -3.97736 |
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 |
| C3 | CZ3 | TRP- 53 | 3.63 | 0 | Hydrophobic |
| C3 | CE2 | TYR- 89 | 4.07 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 112 | 4.24 | 0 | Hydrophobic |
| C6 | CB | MET- 114 | 3.95 | 0 | Hydrophobic |
| C5 | SD | MET- 114 | 3.9 | 0 | Hydrophobic |
| C6 | CE2 | TRP- 143 | 3.36 | 0 | Hydrophobic |
| C5 | CZ2 | TRP- 143 | 3.51 | 0 | Hydrophobic |
| C3 | CH2 | TRP- 143 | 4.19 | 0 | Hydrophobic |
| N11 | O | TRP- 143 | 2.84 | 146.16 | H-Bond (Ligand Donor) |
| C3 | CG | TYR- 185 | 4.2 | 0 | Hydrophobic |
| C7 | SG | CYS- 188 | 3.81 | 0 | Hydrophobic |
| C7 | CZ | TYR- 192 | 3.73 | 0 | Hydrophobic |
| N13 | O | HOH- 2079 | 2.94 | 165.46 | H-Bond (Protein Donor) |
