sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2014-08-21
| Name: | Alcohol dehydrogenase 1 |
|---|---|
| ID: | ADH1_YEAST |
| AC: | P00330 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | 1.1.1.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 96 % |
| D | 4 % |
| B-Factor: | 28.694 |
|---|---|
| Number of residues: | 61 |
| Including | |
| Standard Amino Acids: | 56 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.312 | 698.625 |
| % Hydrophobic | % Polar |
|---|---|
| 57.00 | 43.00 |
| According to VolSite | |
| HET Code: | 8ID |
|---|---|
| Formula: | C21H25IN7O14P2 |
| Molecular weight: | 788.314 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 76.06 % |
| Polar Surface area: | 343.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 18 |
| H-Bond Donors: | 6 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 80.7689 | -18.2925 | -20.2924 |
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 |
| C5N | SG | CYS- 43 | 3.83 | 0 | Hydrophobic |
| C5' | CB | HIS- 44 | 4.08 | 0 | Hydrophobic |
| C3' | CB | HIS- 44 | 3.73 | 0 | Hydrophobic |
| O2N | N | HIS- 44 | 3.23 | 161.33 | H-Bond (Protein Donor) |
| O2' | OG1 | THR- 45 | 2.9 | 158.34 | H-Bond (Protein Donor) |
| O3' | NE2 | HIS- 48 | 2.67 | 159.67 | H-Bond (Protein Donor) |
| C5N | SG | CYS- 153 | 3.66 | 0 | Hydrophobic |
| C4N | CG2 | THR- 157 | 3.27 | 0 | Hydrophobic |
| O1A | N | GLY- 181 | 3.15 | 165.77 | H-Bond (Protein Donor) |
| C5' | CD1 | LEU- 182 | 4.42 | 0 | Hydrophobic |
| C5N | CD2 | LEU- 182 | 3.69 | 0 | Hydrophobic |
| O1N | N | LEU- 182 | 3.1 | 154.8 | H-Bond (Protein Donor) |
| O2B | OD2 | ASP- 201 | 3.34 | 134.02 | H-Bond (Ligand Donor) |
| O3B | OD2 | ASP- 201 | 2.65 | 152.25 | H-Bond (Ligand Donor) |
| O2B | NZ | LYS- 206 | 3.46 | 133.28 | H-Bond (Protein Donor) |
| O3B | NZ | LYS- 206 | 3.12 | 154.11 | H-Bond (Protein Donor) |
| C1B | CB | SER- 246 | 4.15 | 0 | Hydrophobic |
| C5B | CG2 | VAL- 247 | 4.42 | 0 | Hydrophobic |
| I8A | CB | VAL- 247 | 4.21 | 0 | Hydrophobic |
| C5' | CG2 | VAL- 247 | 4.1 | 0 | Hydrophobic |
| N7N | O | VAL- 268 | 2.77 | 173.31 | H-Bond (Ligand Donor) |
| C3N | CG1 | VAL- 268 | 3.77 | 0 | Hydrophobic |
| O3' | N | MET- 270 | 3.21 | 168.2 | H-Bond (Protein Donor) |
| N7N | O | SER- 293 | 3.09 | 148.63 | H-Bond (Ligand Donor) |
| O7N | N | VAL- 295 | 2.73 | 166.84 | H-Bond (Protein Donor) |
| C4N | CG1 | VAL- 295 | 4.26 | 0 | Hydrophobic |
| O2N | CZ | ARG- 340 | 3.63 | 0 | Ionic (Protein Cationic) |
| O2N | NH1 | ARG- 340 | 2.82 | 163.65 | H-Bond (Protein Donor) |
| O1N | O | HOH- 513 | 2.8 | 159.66 | H-Bond (Protein Donor) |
