sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
1999-09-29
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.570 | 6.860 | 7.500 | 0.910 | 7.520 | 3 |
| 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: | 22.546 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | FMN |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.916 | 577.125 |
| % Hydrophobic | % Polar |
|---|---|
| 72.51 | 27.49 |
| According to VolSite | |
| HET Code: | A26 |
|---|---|
| Formula: | C12H9F3N2O2 |
| Molecular weight: | 270.207 g/mol |
| DrugBank ID: | DB08880 |
| Buried Surface Area: | 69.54 % |
| Polar Surface area: | 73.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 49.8316 | 42.8233 | -1.54689 |
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 |
| C4 | CE | MET- 43 | 3.67 | 0 | Hydrophobic |
| C21 | CB | HIS- 56 | 3.74 | 0 | Hydrophobic |
| C1 | CB | ALA- 59 | 3.54 | 0 | Hydrophobic |
| F13 | SD | MET- 111 | 3.96 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 134 | 3.88 | 0 | Hydrophobic |
| O20 | OH | TYR- 356 | 2.81 | 158.64 | H-Bond (Ligand Donor) |
| C21 | CZ | TYR- 356 | 4.37 | 0 | Hydrophobic |
| F14 | CG | LEU- 359 | 3.29 | 0 | Hydrophobic |
| C1 | CG2 | THR- 360 | 4.38 | 0 | Hydrophobic |
| F12 | CG | PRO- 364 | 3.59 | 0 | Hydrophobic |
| C21 | C7M | FMN- 398 | 4.18 | 0 | Hydrophobic |
| O25 | O | HOH- 603 | 2.75 | 179.99 | H-Bond (Protein Donor) |
