sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.440 Å
X-ray
2004-01-08
| Name: | Dihydroorotate dehydrogenase (quinone), mitochondrial |
|---|---|
| ID: | PYRD_RAT |
| AC: | Q63707 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | 1.3.5.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 30.398 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | FMN |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 2.103 | 502.875 |
| % Hydrophobic | % Polar |
|---|---|
| 77.18 | 22.82 |
| According to VolSite | |
| HET Code: | BRF |
|---|---|
| Formula: | C23H14F2NO2 |
| Molecular weight: | 374.360 g/mol |
| DrugBank ID: | DB03523 |
| Buried Surface Area: | 64.03 % |
| Polar Surface area: | 53.02 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 8.57404 | 24.0615 | 118.944 |
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 |
| F2 | CE2 | TYR- 38 | 3.85 | 0 | Hydrophobic |
| F2 | CD2 | LEU- 42 | 3.46 | 0 | Hydrophobic |
| F2 | SD | MET- 43 | 4.17 | 0 | Hydrophobic |
| C1 | CE | MET- 43 | 3.86 | 0 | Hydrophobic |
| C9 | CE | MET- 43 | 3.54 | 0 | Hydrophobic |
| C1 | CB | LEU- 46 | 4.14 | 0 | Hydrophobic |
| F2 | CD2 | LEU- 46 | 4.17 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 46 | 3.8 | 0 | Hydrophobic |
| C1 | CG | GLN- 47 | 4.23 | 0 | Hydrophobic |
| O1 | NE2 | GLN- 47 | 3.5 | 120.18 | H-Bond (Protein Donor) |
| C10 | CB | PRO- 52 | 4.01 | 0 | Hydrophobic |
| F1 | CB | PRO- 52 | 4.14 | 0 | Hydrophobic |
| C4 | CB | ALA- 55 | 3.57 | 0 | Hydrophobic |
| C15 | CB | HIS- 56 | 3.56 | 0 | Hydrophobic |
| C23 | CB | ALA- 59 | 3.54 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 62 | 4.09 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 68 | 3.77 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 134 | 4.21 | 0 | Hydrophobic |
| F1 | CB | VAL- 134 | 4.45 | 0 | Hydrophobic |
| O1 | NE | ARG- 136 | 2.92 | 162.11 | H-Bond (Protein Donor) |
| O2 | NH2 | ARG- 136 | 2.98 | 166.12 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 136 | 3.81 | 0 | Ionic (Protein Cationic) |
| O2 | CZ | ARG- 136 | 3.69 | 0 | Ionic (Protein Cationic) |
| F1 | CG1 | VAL- 143 | 4.14 | 0 | Hydrophobic |
| C11 | CG1 | ILE- 360 | 3.68 | 0 | Hydrophobic |
| C4 | CG2 | ILE- 360 | 3.65 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 360 | 3.54 | 0 | Hydrophobic |
| C21 | CG | PRO- 364 | 3.66 | 0 | Hydrophobic |
| F1 | C7M | FMN- 1398 | 3.98 | 0 | Hydrophobic |
