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
2009-07-07
| 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: | 62.502 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | FMN |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.832 | 327.375 |
| % Hydrophobic | % Polar |
|---|---|
| 77.32 | 22.68 |
| According to VolSite | |
| HET Code: | J5Z |
|---|---|
| Formula: | C13H10F3N5 |
| Molecular weight: | 293.247 g/mol |
| DrugBank ID: | DB08008 |
| Buried Surface Area: | 73.95 % |
| Polar Surface area: | 55.11 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -3.87729 | 28.7915 | 15.032 |
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 |
| C14 | CG | LEU- 172 | 4.09 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 172 | 3.85 | 0 | Hydrophobic |
| C14 | CB | CYS- 175 | 4.4 | 0 | Hydrophobic |
| C14 | CB | LEU- 176 | 4.27 | 0 | Hydrophobic |
| C14 | CB | CYS- 184 | 3.66 | 0 | Hydrophobic |
| N1 | ND1 | HIS- 185 | 2.98 | 132.7 | H-Bond (Ligand Donor) |
| C3 | CB | HIS- 185 | 4.49 | 0 | Hydrophobic |
| C14 | CE1 | PHE- 188 | 4.39 | 0 | Hydrophobic |
| C4 | CB | PHE- 188 | 3.45 | 0 | Hydrophobic |
| F24 | CB | PHE- 188 | 3.79 | 0 | Hydrophobic |
| F24 | CD1 | LEU- 197 | 3.76 | 0 | Hydrophobic |
| C8 | CZ | PHE- 227 | 4.41 | 0 | Hydrophobic |
| F23 | CE2 | PHE- 227 | 3.92 | 0 | Hydrophobic |
| F23 | CD1 | LEU- 240 | 3.53 | 0 | Hydrophobic |
| N5 | NH1 | ARG- 265 | 3.22 | 127.44 | H-Bond (Protein Donor) |
| C10 | CB | LEU- 531 | 4.33 | 0 | Hydrophobic |
| F22 | CD2 | LEU- 531 | 3.66 | 0 | Hydrophobic |
| F23 | CD2 | LEU- 531 | 4.44 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 532 | 4.34 | 0 | Hydrophobic |
| F22 | SD | MET- 536 | 4.3 | 0 | Hydrophobic |
| F24 | CE | MET- 536 | 3.59 | 0 | Hydrophobic |
