sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.240 Å
X-ray
2014-04-11
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.660 | 6.660 | 6.660 | 0.000 | 6.660 | 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 |
|---|---|
| C | 62 % |
| D | 38 % |
| B-Factor: | 39.204 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.392 | 695.250 |
| % Hydrophobic | % Polar |
|---|---|
| 55.83 | 44.17 |
| According to VolSite | |
| HET Code: | TH4 |
|---|---|
| Formula: | C10H9ClN4S |
| Molecular weight: | 252.723 g/mol |
| DrugBank ID: | DB08620 |
| Buried Surface Area: | 81.08 % |
| Polar Surface area: | 77.58 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 0 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 22.8228 | 21.9377 | -34.8298 |
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 |
| C8 | CZ3 | TRP- 53 | 4.42 | 0 | Hydrophobic |
| C12 | CZ | TYR- 89 | 3.68 | 0 | Hydrophobic |
| CL7 | CB | ARG- 104 | 3.63 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 112 | 3.85 | 0 | Hydrophobic |
| CL7 | CG | LEU- 112 | 4.15 | 0 | Hydrophobic |
| C8 | SD | MET- 114 | 3.94 | 0 | Hydrophobic |
| C4 | CE | MET- 114 | 4.04 | 0 | Hydrophobic |
| C8 | CZ2 | TRP- 143 | 4.32 | 0 | Hydrophobic |
| C13 | CE3 | TRP- 143 | 3.46 | 0 | Hydrophobic |
| CL7 | CG2 | THR- 144 | 3.56 | 0 | Hydrophobic |
| S11 | CG2 | VAL- 183 | 4.02 | 0 | Hydrophobic |
| C5 | SG | CYS- 188 | 4.12 | 0 | Hydrophobic |
| C12 | CG | TYR- 192 | 4.2 | 0 | Hydrophobic |
| S11 | CD1 | TYR- 192 | 3.38 | 0 | Hydrophobic |
| N2 | O | HOH- 401 | 2.72 | 151.61 | H-Bond (Protein Donor) |
