sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.060 Å
X-ray
2006-10-10
| Name: | Dihydroflavonol 4-reductase |
|---|---|
| ID: | DFRA_VITVI |
| AC: | P51110 |
| Organism: | Vitis vinifera |
| Reign: | Eukaryota |
| TaxID: | 29760 |
| EC Number: | 1.1.1.219 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 4 % |
| D | 96 % |
| B-Factor: | 36.184 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.123 | 1603.125 |
| % Hydrophobic | % Polar |
|---|---|
| 46.95 | 53.05 |
| According to VolSite | |
| HET Code: | MYC |
|---|---|
| Formula: | C15H8O8 |
| Molecular weight: | 316.219 g/mol |
| DrugBank ID: | DB02375 |
| Buried Surface Area: | 54.91 % |
| Polar Surface area: | 153.34 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -9.2887 | -9.32257 | 43.2785 |
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 |
| C19 | SD | MET- 88 | 4.06 | 0 | Hydrophobic |
| C17 | CB | SER- 128 | 3.98 | 0 | Hydrophobic |
| C1 | CG2 | THR- 159 | 3.83 | 0 | Hydrophobic |
| C3 | CB | ALA- 160 | 4.11 | 0 | Hydrophobic |
| C5 | CB | ALA- 160 | 3.46 | 0 | Hydrophobic |
| C15 | CB | ALA- 160 | 4.41 | 0 | Hydrophobic |
| C17 | CB | TYR- 163 | 3.67 | 0 | Hydrophobic |
| C17 | CG | LYS- 167 | 4.45 | 0 | Hydrophobic |
| C5 | CG1 | ILE- 222 | 3.47 | 0 | Hydrophobic |
| C18 | C2D | NAP- 4340 | 4.39 | 0 | Hydrophobic |
| O23 | O2D | NAP- 4340 | 2.77 | 166.69 | H-Bond (Protein Donor) |
