sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.690 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 | 43 % |
| D | 57 % |
| B-Factor: | 43.617 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.004 | 691.875 |
| % Hydrophobic | % Polar |
|---|---|
| 42.93 | 57.07 |
| According to VolSite | |
| HET Code: | TH4 |
|---|---|
| Formula: | C10H9ClN4S |
| Molecular weight: | 252.723 g/mol |
| DrugBank ID: | DB08620 |
| Buried Surface Area: | 71.68 % |
| 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 |
|---|---|---|
| 24.3994 | 22.2933 | -35.1131 |
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 |
| S11 | CE3 | TRP- 53 | 3.35 | 0 | Hydrophobic |
| C6 | CB | ARG- 104 | 4.24 | 0 | Hydrophobic |
| CL7 | CB | ARG- 104 | 3.48 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 112 | 4.07 | 0 | Hydrophobic |
| CL7 | CG | LEU- 112 | 3.98 | 0 | Hydrophobic |
| C5 | CE | MET- 114 | 4.43 | 0 | Hydrophobic |
| S11 | SD | MET- 114 | 3.47 | 0 | Hydrophobic |
| C13 | CZ2 | TRP- 143 | 3.59 | 0 | Hydrophobic |
| C12 | CH2 | TRP- 143 | 3.4 | 0 | Hydrophobic |
| CL7 | CG2 | THR- 144 | 4.36 | 0 | Hydrophobic |
| C8 | CE1 | TYR- 185 | 3.89 | 0 | Hydrophobic |
| S11 | CE2 | TYR- 185 | 3.92 | 0 | Hydrophobic |
| C13 | CZ | TYR- 185 | 3.93 | 0 | Hydrophobic |
| C8 | CZ | TYR- 192 | 3.88 | 0 | Hydrophobic |
| N2 | O | HOH- 401 | 2.95 | 162.02 | H-Bond (Protein Donor) |
