sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2005-09-14
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.550 | 5.550 | 5.550 | 0.000 | 5.550 | 1 |
| 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: | 28.041 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | FMN |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.830 | 526.500 |
| % Hydrophobic | % Polar |
|---|---|
| 71.79 | 28.21 |
| According to VolSite | |
| HET Code: | 201 |
|---|---|
| Formula: | C20H14NO3 |
| Molecular weight: | 316.330 g/mol |
| DrugBank ID: | DB04583 |
| Buried Surface Area: | 65.51 % |
| Polar Surface area: | 83.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -33.1576 | -12.0568 | 2.38787 |
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 |
| C23 | CE | MET- 43 | 3.85 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 46 | 3.63 | 0 | Hydrophobic |
| O2 | NE2 | GLN- 47 | 2.99 | 151.95 | H-Bond (Protein Donor) |
| C4 | CB | ALA- 55 | 3.66 | 0 | Hydrophobic |
| C7 | CB | HIS- 56 | 4.12 | 0 | Hydrophobic |
| C1 | CB | ALA- 59 | 4.05 | 0 | Hydrophobic |
| C23 | CB | ALA- 59 | 3.44 | 0 | Hydrophobic |
| C8 | CB | ALA- 59 | 3.44 | 0 | Hydrophobic |
| C20 | CB | PHE- 62 | 4.12 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 68 | 3.64 | 0 | Hydrophobic |
| O1 | NH1 | ARG- 136 | 3.2 | 128.71 | H-Bond (Protein Donor) |
| O1 | NE | ARG- 136 | 2.58 | 167.17 | H-Bond (Protein Donor) |
| O2 | NH1 | ARG- 136 | 3.01 | 124.21 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 136 | 3.31 | 0 | Ionic (Protein Cationic) |
| O2 | CZ | ARG- 136 | 3.59 | 0 | Ionic (Protein Cationic) |
| N1 | OH | TYR- 356 | 2.55 | 156 | H-Bond (Ligand Donor) |
| C9 | CG | LEU- 359 | 4.31 | 0 | Hydrophobic |
| C7 | CG2 | THR- 360 | 3.5 | 0 | Hydrophobic |
| C6 | CB | THR- 360 | 3.6 | 0 | Hydrophobic |
| C18 | CG | PRO- 364 | 3.79 | 0 | Hydrophobic |
