sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2010-08-02
| 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: | 69.229 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | FMN |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.241 | 334.125 |
| % Hydrophobic | % Polar |
|---|---|
| 70.71 | 29.29 |
| According to VolSite | |
| HET Code: | O8A |
|---|---|
| Formula: | C17H14F3N3O2S |
| Molecular weight: | 381.372 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.86 % |
| Polar Surface area: | 84.39 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 28.5582 | -10.2866 | 17.0641 |
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 |
| F1 | CD1 | TYR- 168 | 3.51 | 0 | Hydrophobic |
| F3 | CG | PHE- 171 | 3.57 | 0 | Hydrophobic |
| C8 | CB | PHE- 171 | 3.64 | 0 | Hydrophobic |
| C5 | CB | PHE- 171 | 4.39 | 0 | Hydrophobic |
| S1 | CD1 | LEU- 172 | 3.7 | 0 | Hydrophobic |
| C6 | CB | LEU- 172 | 3.85 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 172 | 4.26 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 172 | 3.67 | 0 | Hydrophobic |
| C8 | SG | CYS- 175 | 4.43 | 0 | Hydrophobic |
| C4 | SG | CYS- 175 | 3.79 | 0 | Hydrophobic |
| S1 | CB | CYS- 184 | 4.03 | 0 | Hydrophobic |
| C3 | CB | CYS- 184 | 4.3 | 0 | Hydrophobic |
| N3 | ND1 | HIS- 185 | 3.04 | 138.13 | H-Bond (Ligand Donor) |
| F2 | CG | LEU- 187 | 3.35 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 187 | 4.43 | 0 | Hydrophobic |
| C9 | CD1 | PHE- 188 | 3.88 | 0 | Hydrophobic |
| C3 | CB | PHE- 188 | 4.01 | 0 | Hydrophobic |
| F1 | CD1 | LEU- 191 | 3.41 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 263 | 3.57 | 0 | Hydrophobic |
| O2 | NH1 | ARG- 265 | 2.76 | 144.87 | H-Bond (Protein Donor) |
| C17 | CD | ARG- 265 | 3.77 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 272 | 3.87 | 0 | Hydrophobic |
| C16 | CE2 | TYR- 528 | 4.42 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 532 | 3.93 | 0 | Hydrophobic |
| C6 | CE | MET- 536 | 4.26 | 0 | Hydrophobic |
| C9 | CG | MET- 536 | 4.45 | 0 | Hydrophobic |
| C16 | C7M | FMN- 1002 | 4.26 | 0 | Hydrophobic |
