sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.850 Å
X-ray
2012-11-20
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 14.058 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | FMN |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.100 | 567.000 |
| % Hydrophobic | % Polar |
|---|---|
| 30.36 | 69.64 |
| According to VolSite | |
| HET Code: | YRO |
|---|---|
| Formula: | C11H15N2O4 |
| Molecular weight: | 239.248 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 78.24 % |
| Polar Surface area: | 98.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 39.9178 | -12.9898 | -13.1649 |
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 |
| OAD | NZ | LYS- 43 | 2.97 | 145.13 | H-Bond (Protein Donor) |
| OAD | NZ | LYS- 43 | 2.97 | 0 | Ionic (Protein Cationic) |
| NAJ | OD1 | ASN- 67 | 2.92 | 172.85 | H-Bond (Ligand Donor) |
| OAE | ND2 | ASN- 67 | 2.95 | 171.6 | H-Bond (Protein Donor) |
| OAG | N | GLY- 70 | 3.07 | 142.84 | H-Bond (Protein Donor) |
| OAD | N | LEU- 71 | 2.93 | 144.64 | H-Bond (Protein Donor) |
| CAA | CB | LEU- 71 | 4.03 | 0 | Hydrophobic |
| CAH | CD1 | LEU- 71 | 3.69 | 0 | Hydrophobic |
| OAF | ND2 | ASN- 127 | 2.98 | 162.88 | H-Bond (Protein Donor) |
| CAB | CB | SER- 129 | 4.41 | 0 | Hydrophobic |
| CAB | CB | CYS- 130 | 4.25 | 0 | Hydrophobic |
| CAB | CG | PRO- 131 | 4.37 | 0 | Hydrophobic |
| CAA | CG | PRO- 131 | 4.16 | 0 | Hydrophobic |
| NAK | OD1 | ASN- 194 | 2.72 | 175.91 | H-Bond (Ligand Donor) |
| OAF | ND2 | ASN- 194 | 2.87 | 158.31 | H-Bond (Protein Donor) |
| OAE | OG | SER- 195 | 2.64 | 151.63 | H-Bond (Protein Donor) |
