sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2014-11-05
| Name: | Alcohol dehydrogenase class-P |
|---|---|
| ID: | ADH1_ARATH |
| AC: | P06525 |
| Organism: | Arabidopsis thaliana |
| Reign: | Eukaryota |
| TaxID: | 3702 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 2 % |
| B | 98 % |
| B-Factor: | 35.110 |
|---|---|
| Number of residues: | 52 |
| Including | |
| Standard Amino Acids: | 51 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.364 | 999.000 |
| % Hydrophobic | % Polar |
|---|---|
| 47.64 | 52.36 |
| According to VolSite | |
| HET Code: | NAD |
|---|---|
| Formula: | C21H26N7O14P2 |
| Molecular weight: | 662.417 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.87 % |
| 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 |
|---|---|---|
| -29.4426 | 56.5384 | -27.1846 |
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- 47 | 3.8 | 0 | Hydrophobic |
| O1N | N | HIS- 48 | 3.46 | 163.5 | H-Bond (Protein Donor) |
| C3D | CB | HIS- 48 | 4.27 | 0 | Hydrophobic |
| O2D | OG1 | THR- 49 | 2.92 | 168.34 | H-Bond (Protein Donor) |
| C5N | SG | CYS- 177 | 3.2 | 0 | Hydrophobic |
| C3N | CG2 | THR- 181 | 3.63 | 0 | Hydrophobic |
| O2N | N | VAL- 206 | 2.82 | 170.68 | H-Bond (Protein Donor) |
| C5N | CG2 | VAL- 206 | 3.69 | 0 | Hydrophobic |
| C5D | CG2 | VAL- 206 | 3.77 | 0 | Hydrophobic |
| O3B | OD2 | ASP- 226 | 3 | 174.66 | H-Bond (Ligand Donor) |
| O2B | OD2 | ASP- 226 | 3.09 | 147.24 | H-Bond (Ligand Donor) |
| O2B | OD1 | ASP- 226 | 2.62 | 146.85 | H-Bond (Ligand Donor) |
| C3B | CD | ARG- 231 | 4.3 | 0 | Hydrophobic |
| O3B | NH1 | ARG- 231 | 2.56 | 135.48 | H-Bond (Protein Donor) |
| C1B | CG2 | THR- 272 | 4.25 | 0 | Hydrophobic |
| N7N | O | VAL- 295 | 3.22 | 158.45 | H-Bond (Ligand Donor) |
| O7N | N | PHE- 322 | 2.82 | 129.51 | H-Bond (Protein Donor) |
| O1N | CZ | ARG- 372 | 3.84 | 0 | Ionic (Protein Cationic) |
| O1N | NH2 | ARG- 372 | 3.37 | 151.56 | H-Bond (Protein Donor) |
| O1N | NH1 | ARG- 372 | 3.32 | 153.83 | H-Bond (Protein Donor) |
