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
2007-05-04
| Name: | Dihydroorotate dehydrogenase (quinone), mitochondrial |
|---|---|
| ID: | PYRD_HUMAN |
| AC: | Q02127 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.3.5.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 15.200 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | FMN |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.943 | 725.625 |
| % Hydrophobic | % Polar |
|---|---|
| 75.81 | 24.19 |
| According to VolSite | |
| HET Code: | 238 |
|---|---|
| Formula: | C23H14ClFNO2 |
| Molecular weight: | 390.814 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.66 % |
| 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 |
|---|---|---|
| 51.2308 | 43.3616 | -2.33229 |
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 | CE2 | TYR- 38 | 3.67 | 0 | Hydrophobic |
| F1 | CD2 | LEU- 42 | 3.72 | 0 | Hydrophobic |
| F1 | SD | MET- 43 | 3.65 | 0 | Hydrophobic |
| C1 | CE | MET- 43 | 3.66 | 0 | Hydrophobic |
| C23 | CE | MET- 43 | 3.67 | 0 | Hydrophobic |
| F1 | CD2 | LEU- 46 | 4.34 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 46 | 3.84 | 0 | Hydrophobic |
| O1 | NE2 | GLN- 47 | 2.94 | 171.27 | H-Bond (Protein Donor) |
| C1 | CG | GLN- 47 | 4 | 0 | Hydrophobic |
| CL1 | CB | PRO- 52 | 4.06 | 0 | Hydrophobic |
| C10 | CB | PRO- 52 | 4.01 | 0 | Hydrophobic |
| C2 | CB | ALA- 55 | 3.78 | 0 | Hydrophobic |
| C15 | CB | HIS- 56 | 3.51 | 0 | Hydrophobic |
| C18 | CB | ALA- 59 | 4.33 | 0 | Hydrophobic |
| C23 | CB | ALA- 59 | 3.53 | 0 | Hydrophobic |
| C20 | CB | PHE- 62 | 4 | 0 | Hydrophobic |
| C20 | CD1 | LEU- 68 | 3.32 | 0 | Hydrophobic |
| C20 | CE | MET- 111 | 4.31 | 0 | Hydrophobic |
| CL1 | CG1 | VAL- 134 | 3.96 | 0 | Hydrophobic |
| O2 | NH1 | ARG- 136 | 2.66 | 176.51 | H-Bond (Protein Donor) |
| O2 | NE | ARG- 136 | 3.47 | 129.23 | H-Bond (Protein Donor) |
| O1 | NE | ARG- 136 | 2.89 | 177.16 | H-Bond (Protein Donor) |
| O2 | CZ | ARG- 136 | 3.49 | 0 | Ionic (Protein Cationic) |
| O1 | CZ | ARG- 136 | 3.71 | 0 | Ionic (Protein Cationic) |
| CL1 | CG1 | VAL- 143 | 4.1 | 0 | Hydrophobic |
| C9 | CG | LEU- 359 | 4.22 | 0 | Hydrophobic |
| C4 | CB | THR- 360 | 3.76 | 0 | Hydrophobic |
| C6 | CG2 | THR- 360 | 3.55 | 0 | Hydrophobic |
| C21 | CG | PRO- 364 | 3.63 | 0 | Hydrophobic |
| CL1 | C7M | FMN- 398 | 3.85 | 0 | Hydrophobic |
