sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2012-03-06
| 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 |
|---|---|
| C | 48 % |
| D | 52 % |
| B-Factor: | 29.787 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.145 | 621.000 |
| % Hydrophobic | % Polar |
|---|---|
| 53.26 | 46.74 |
| According to VolSite | |
| HET Code: | IZN |
|---|---|
| Formula: | C16H22NO3 |
| Molecular weight: | 276.351 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 79.25 % |
| Polar Surface area: | 39.97 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -8.09865 | 14.0008 | -1.1238 |
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 | CZ3 | TRP- 53 | 3.88 | 0 | Hydrophobic |
| C13 | CZ3 | TRP- 53 | 3.94 | 0 | Hydrophobic |
| O1 | NE2 | GLN- 55 | 3.05 | 134.44 | H-Bond (Protein Donor) |
| C2 | CE2 | TYR- 89 | 4.02 | 0 | Hydrophobic |
| C7 | CB | ARG- 104 | 4.27 | 0 | Hydrophobic |
| C16 | CB | ARG- 104 | 4.14 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 112 | 4.07 | 0 | Hydrophobic |
| C16 | CG | LEU- 112 | 3.8 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 112 | 4.01 | 0 | Hydrophobic |
| C13 | SD | MET- 114 | 3.56 | 0 | Hydrophobic |
| C15 | SD | MET- 114 | 3.49 | 0 | Hydrophobic |
| C16 | CB | MET- 114 | 4.25 | 0 | Hydrophobic |
| C6 | CB | MET- 114 | 4.2 | 0 | Hydrophobic |
| N1 | O | TRP- 143 | 2.82 | 167.3 | H-Bond (Ligand Donor) |
| C2 | CH2 | TRP- 143 | 4.26 | 0 | Hydrophobic |
| C5 | CE2 | TRP- 143 | 3.91 | 0 | Hydrophobic |
| C16 | CG2 | THR- 144 | 4.38 | 0 | Hydrophobic |
| C7 | CG2 | THR- 144 | 4.32 | 0 | Hydrophobic |
| C13 | CZ | TYR- 164 | 4.34 | 0 | Hydrophobic |
| C2 | CE1 | TYR- 185 | 4 | 0 | Hydrophobic |
| C9 | CD2 | TYR- 185 | 3.84 | 0 | Hydrophobic |
| C13 | CD1 | TYR- 185 | 4.05 | 0 | Hydrophobic |
| C9 | SG | CYS- 187 | 4.01 | 0 | Hydrophobic |
| C15 | SG | CYS- 187 | 3.42 | 0 | Hydrophobic |
| C9 | SG | CYS- 188 | 4.02 | 0 | Hydrophobic |
| C9 | CZ | TYR- 192 | 3.52 | 0 | Hydrophobic |
| O3 | O | HOH- 2060 | 3.38 | 150.6 | H-Bond (Protein Donor) |
