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
2004-06-27
| Name: | Dihydroorotate dehydrogenase (quinone), mitochondrial |
|---|---|
| ID: | PYRD_PLAF7 |
| AC: | Q08210 |
| Organism: | Plasmodium falciparum |
| Reign: | Eukaryota |
| TaxID: | 36329 |
| EC Number: | 1.3.5.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 25.577 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | FMN |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.043 | 411.750 |
| % Hydrophobic | % Polar |
|---|---|
| 53.28 | 46.72 |
| According to VolSite | |
| HET Code: | A26 |
|---|---|
| Formula: | C12H9F3N2O2 |
| Molecular weight: | 270.207 g/mol |
| DrugBank ID: | DB08880 |
| Buried Surface Area: | 76.51 % |
| Polar Surface area: | 73.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 38.0317 | 34.8801 | 36.6769 |
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 |
| F14 | CE2 | PHE- 171 | 3.39 | 0 | Hydrophobic |
| F13 | CD2 | PHE- 171 | 3.73 | 0 | Hydrophobic |
| F13 | CD1 | LEU- 172 | 3.72 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 172 | 3.67 | 0 | Hydrophobic |
| C2 | CB | CYS- 175 | 4.45 | 0 | Hydrophobic |
| C1 | SG | CYS- 184 | 4.39 | 0 | Hydrophobic |
| F12 | CE1 | PHE- 188 | 4.03 | 0 | Hydrophobic |
| C4 | CD1 | PHE- 188 | 3.47 | 0 | Hydrophobic |
| C4 | CB | PHE- 188 | 3.87 | 0 | Hydrophobic |
| F14 | CD1 | PHE- 188 | 3.65 | 0 | Hydrophobic |
| C21 | CG2 | ILE- 263 | 3.68 | 0 | Hydrophobic |
| O20 | NH1 | ARG- 265 | 2.9 | 139.42 | H-Bond (Protein Donor) |
| C21 | CG | ARG- 265 | 3.39 | 0 | Hydrophobic |
| N26 | OH | TYR- 528 | 2.69 | 170.65 | H-Bond (Protein Donor) |
| C21 | CG1 | VAL- 532 | 4.19 | 0 | Hydrophobic |
| F12 | CG | MET- 536 | 3.32 | 0 | Hydrophobic |
| F14 | CE | MET- 536 | 3.26 | 0 | Hydrophobic |
