sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2001-10-30
| Name: | Leucoanthocyanidin dioxygenase |
|---|---|
| ID: | LDOX_ARATH |
| AC: | Q96323 |
| Organism: | Arabidopsis thaliana |
| Reign: | Eukaryota |
| TaxID: | 3702 |
| EC Number: | 1.14.11.19 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 17.837 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | FE |
| Ligandability | Volume (Å3) |
|---|---|
| 0.904 | 1073.250 |
| % Hydrophobic | % Polar |
|---|---|
| 48.43 | 51.57 |
| According to VolSite | |
| HET Code: | DQH |
|---|---|
| Formula: | C15H11O7 |
| Molecular weight: | 303.244 g/mol |
| DrugBank ID: | DB02224 |
| Buried Surface Area: | 55.13 % |
| Polar Surface area: | 130.28 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 15.1067 | 27.423 | 2.70277 |
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 |
| O23 | OH | TYR- 142 | 2.69 | 142.1 | H-Bond (Ligand Donor) |
| O24 | OH | TYR- 142 | 2.64 | 140.87 | H-Bond (Ligand Donor) |
| C16 | CB | PHE- 144 | 4.08 | 0 | Hydrophobic |
| O27 | NZ | LYS- 213 | 3.02 | 150.88 | H-Bond (Protein Donor) |
| C10 | CD | LYS- 213 | 3.9 | 0 | Hydrophobic |
| C14 | CD | LYS- 213 | 4.13 | 0 | Hydrophobic |
| C2 | CB | ASP- 234 | 4.32 | 0 | Hydrophobic |
| O30 | N | VAL- 235 | 3.38 | 136.26 | H-Bond (Protein Donor) |
| C1 | CG2 | VAL- 235 | 3.47 | 0 | Hydrophobic |
| C1 | CB | SER- 236 | 3.89 | 0 | Hydrophobic |
| C10 | CZ | PHE- 304 | 3.91 | 0 | Hydrophobic |
| C6 | CB | PHE- 304 | 3.59 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 304 | 3.59 | 0 | Aromatic Face/Face |
| C6 | CG | GLU- 306 | 4.44 | 0 | Hydrophobic |
| O24 | O | HOH- 2206 | 2.64 | 179.95 | H-Bond (Protein Donor) |
