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
2013-08-01
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.770 | 8.770 | 8.770 | 0.000 | 8.770 | 1 |
| Name: | Acetylcholinesterase |
|---|---|
| ID: | ACES_HUMAN |
| AC: | P22303 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.1.1.7 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 44.303 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.042 | 749.250 |
| % Hydrophobic | % Polar |
|---|---|
| 49.55 | 50.45 |
| According to VolSite | |
| HET Code: | 1YK |
|---|---|
| Formula: | C29H34O9 |
| Molecular weight: | 526.575 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 53.63 % |
| Polar Surface area: | 120.75 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 11.0322 | -55.8763 | -23.8338 |
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 |
| C29 | CZ | TYR- 72 | 4.33 | 0 | Hydrophobic |
| C16 | CB | TRP- 86 | 4.2 | 0 | Hydrophobic |
| C22 | CD2 | TRP- 86 | 4.33 | 0 | Hydrophobic |
| C24 | CE3 | TRP- 86 | 3.39 | 0 | Hydrophobic |
| C23 | CE2 | TRP- 86 | 3.5 | 0 | Hydrophobic |
| O9 | OH | TYR- 124 | 2.71 | 146.78 | H-Bond (Ligand Donor) |
| C28 | CB | TRP- 286 | 3.63 | 0 | Hydrophobic |
| DuAr | DuAr | TRP- 286 | 3.75 | 0 | Aromatic Face/Face |
| C12 | CE1 | PHE- 297 | 4.43 | 0 | Hydrophobic |
| C26 | CE2 | TYR- 337 | 3.41 | 0 | Hydrophobic |
| C16 | CZ | TYR- 337 | 4.39 | 0 | Hydrophobic |
| C23 | CE1 | TYR- 337 | 3.83 | 0 | Hydrophobic |
| C25 | CD1 | TYR- 337 | 3.88 | 0 | Hydrophobic |
| C12 | CE2 | PHE- 338 | 3.57 | 0 | Hydrophobic |
| C25 | CE2 | PHE- 338 | 3.92 | 0 | Hydrophobic |
| C26 | CE2 | TYR- 341 | 3.43 | 0 | Hydrophobic |
| C1 | CB | TYR- 341 | 4.24 | 0 | Hydrophobic |
