sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.580 Å
X-ray
2012-11-30
| Name: | Dihydroorotate dehydrogenase (fumarate) |
|---|---|
| ID: | PYRD_TRYCC |
| AC: | Q4D3W2 |
| Organism: | Trypanosoma cruzi |
| Reign: | Eukaryota |
| TaxID: | 353153 |
| EC Number: | 1.3.98.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 12.357 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | FMN |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.154 | 546.750 |
| % Hydrophobic | % Polar |
|---|---|
| 28.40 | 71.60 |
| According to VolSite | |
| HET Code: | ZRO |
|---|---|
| Formula: | C14H10F3N2O4 |
| Molecular weight: | 327.235 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.23 % |
| Polar Surface area: | 98.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -6.03717 | -14.3831 | 11.0787 |
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 |
| OAA | NZ | LYS- 43 | 3.13 | 152.28 | H-Bond (Protein Donor) |
| OAA | NZ | LYS- 43 | 3.13 | 0 | Ionic (Protein Cationic) |
| FAF | CG2 | THR- 46 | 3.91 | 0 | Hydrophobic |
| FAE | CD | ARG- 50 | 3.54 | 0 | Hydrophobic |
| NAN | OD1 | ASN- 67 | 2.91 | 167.59 | H-Bond (Ligand Donor) |
| OAB | ND2 | ASN- 67 | 2.95 | 172.5 | H-Bond (Protein Donor) |
| OAD | N | GLY- 70 | 3.04 | 144.93 | H-Bond (Protein Donor) |
| OAA | N | LEU- 71 | 2.88 | 148.15 | H-Bond (Protein Donor) |
| CAK | CD2 | LEU- 71 | 3.89 | 0 | Hydrophobic |
| CAJ | CB | LEU- 71 | 3.71 | 0 | Hydrophobic |
| FAE | CD2 | LEU- 71 | 3.28 | 0 | Hydrophobic |
| CAI | CD1 | LEU- 71 | 3.49 | 0 | Hydrophobic |
| CAI | CB | SER- 99 | 3.78 | 0 | Hydrophobic |
| FAF | CD2 | LEU- 101 | 3.24 | 0 | Hydrophobic |
| OAC | ND2 | ASN- 127 | 2.91 | 161.81 | H-Bond (Protein Donor) |
| CAK | CB | CYS- 130 | 4.33 | 0 | Hydrophobic |
| CAR | CG | PRO- 131 | 3.94 | 0 | Hydrophobic |
| FAG | CG | PRO- 131 | 3.3 | 0 | Hydrophobic |
| NAO | OD1 | ASN- 194 | 2.78 | 178.34 | H-Bond (Ligand Donor) |
| OAC | ND2 | ASN- 194 | 2.88 | 154.92 | H-Bond (Protein Donor) |
| OAB | OG | SER- 195 | 2.76 | 152.15 | H-Bond (Protein Donor) |
