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
2004-01-06
| 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: | 30.997 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | FMN |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 2.185 | 536.625 |
| % Hydrophobic | % Polar |
|---|---|
| 80.50 | 19.50 |
| According to VolSite | |
| HET Code: | AFI |
|---|---|
| Formula: | C22H19ClO3 |
| Molecular weight: | 366.837 g/mol |
| DrugBank ID: | DB04281 |
| Buried Surface Area: | 67.72 % |
| Polar Surface area: | 57.53 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 77.3818 | 47.7405 | 138.12 |
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 |
| CL | CB | GLU- 40 | 3.6 | 0 | Hydrophobic |
| C14 | CG | MET- 43 | 4.14 | 0 | Hydrophobic |
| C17 | CG | MET- 43 | 3.67 | 0 | Hydrophobic |
| C20 | CB | MET- 43 | 3.59 | 0 | Hydrophobic |
| C22 | CG | MET- 43 | 3.33 | 0 | Hydrophobic |
| C19 | CG | PRO- 44 | 3.67 | 0 | Hydrophobic |
| O6 | NE2 | GLN- 47 | 2.83 | 143.43 | H-Bond (Protein Donor) |
| C14 | CB | GLN- 47 | 4.26 | 0 | Hydrophobic |
| C15 | CG | GLN- 47 | 3.58 | 0 | Hydrophobic |
| C5 | CB | PRO- 52 | 4.03 | 0 | Hydrophobic |
| C15 | CB | ALA- 55 | 4.08 | 0 | Hydrophobic |
| C8 | CB | HIS- 56 | 3.44 | 0 | Hydrophobic |
| C12 | CB | ALA- 59 | 4.49 | 0 | Hydrophobic |
| C14 | CB | ALA- 59 | 4.24 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 68 | 3.8 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 134 | 3.72 | 0 | Hydrophobic |
| O2 | NH2 | ARG- 136 | 3.19 | 121.13 | H-Bond (Protein Donor) |
| O2 | NE | ARG- 136 | 2.82 | 131.24 | H-Bond (Protein Donor) |
| O6 | NH2 | ARG- 136 | 2.76 | 152.17 | H-Bond (Protein Donor) |
| C9 | CG1 | ILE- 360 | 3.48 | 0 | Hydrophobic |
| C11 | CG1 | ILE- 360 | 4.32 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 360 | 3.48 | 0 | Hydrophobic |
| C20 | CG | PRO- 364 | 3.8 | 0 | Hydrophobic |
| C21 | CG | PRO- 364 | 3.39 | 0 | Hydrophobic |
| C6 | C7M | FMN- 398 | 3.68 | 0 | Hydrophobic |
