sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.540 Å
X-ray
2014-04-11
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.010 | 6.010 | 6.010 | 0.000 | 6.010 | 1 |
| 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 |
|---|---|
| B | 43 % |
| C | 57 % |
| B-Factor: | 35.775 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.723 | 648.000 |
| % Hydrophobic | % Polar |
|---|---|
| 48.96 | 51.04 |
| According to VolSite | |
| HET Code: | IM4 |
|---|---|
| Formula: | C9H10ClN5O2 |
| Molecular weight: | 255.661 g/mol |
| DrugBank ID: | DB11421 |
| Buried Surface Area: | 72.51 % |
| Polar Surface area: | 86.34 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 9.27088 | -4.63882 | -34.1824 |
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 |
| C6 | CB | ARG- 104 | 4.11 | 0 | Hydrophobic |
| CL7 | CB | ARG- 104 | 3.81 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 112 | 4.05 | 0 | Hydrophobic |
| CL7 | CG | LEU- 112 | 3.72 | 0 | Hydrophobic |
| CL7 | CB | MET- 114 | 4.46 | 0 | Hydrophobic |
| C4 | CE | MET- 114 | 4.39 | 0 | Hydrophobic |
| C13 | CZ3 | TRP- 143 | 3.83 | 0 | Hydrophobic |
| C6 | CG2 | THR- 144 | 4.41 | 0 | Hydrophobic |
| CL7 | CG2 | THR- 144 | 4.46 | 0 | Hydrophobic |
| C13 | CZ | TYR- 185 | 4.17 | 0 | Hydrophobic |
| C8 | CZ | TYR- 192 | 3.5 | 0 | Hydrophobic |
| N2 | O | HOH- 403 | 2.65 | 158.47 | H-Bond (Protein Donor) |
