sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.250 Å
X-ray
2012-12-05
| 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: | 21.944 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | FMN |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.049 | 570.375 |
| % Hydrophobic | % Polar |
|---|---|
| 30.77 | 69.23 |
| According to VolSite | |
| HET Code: | ROU |
|---|---|
| Formula: | C15H9F6N2O4 |
| Molecular weight: | 395.233 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.6 % |
| 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: | 6 |
| X | Y | Z |
|---|---|---|
| -4.78337 | -13.7656 | 11.9025 |
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 | 3.35 | 159.1 | H-Bond (Protein Donor) |
| OAA | NZ | LYS- 43 | 3.35 | 0 | Ionic (Protein Cationic) |
| NAP | OD1 | ASN- 67 | 3 | 165.96 | H-Bond (Ligand Donor) |
| OAB | ND2 | ASN- 67 | 2.88 | 169.57 | H-Bond (Protein Donor) |
| OAD | N | MET- 69 | 3.22 | 127.13 | H-Bond (Protein Donor) |
| OAD | N | GLY- 70 | 3.2 | 146.22 | H-Bond (Protein Donor) |
| OAA | N | LEU- 71 | 3.03 | 134.57 | H-Bond (Protein Donor) |
| CAO | CD1 | LEU- 71 | 4.02 | 0 | Hydrophobic |
| CAN | CD2 | LEU- 71 | 4.42 | 0 | Hydrophobic |
| FAF | CD2 | LEU- 71 | 3.86 | 0 | Hydrophobic |
| FAE | CB | LEU- 71 | 3.58 | 0 | Hydrophobic |
| FAF | CD2 | LEU- 101 | 3.41 | 0 | Hydrophobic |
| OAC | ND2 | ASN- 127 | 3.08 | 159.18 | H-Bond (Protein Donor) |
| CAK | SG | CYS- 130 | 3.99 | 0 | Hydrophobic |
| FAG | CG | PRO- 131 | 4.24 | 0 | Hydrophobic |
| FAJ | CG | PRO- 131 | 4.18 | 0 | Hydrophobic |
| CAM | CG | PRO- 131 | 4.21 | 0 | Hydrophobic |
| NAQ | OD1 | ASN- 194 | 2.64 | 172.36 | H-Bond (Ligand Donor) |
| OAC | ND2 | ASN- 194 | 2.77 | 142.7 | H-Bond (Protein Donor) |
| FAI | CD | LYS- 214 | 4.11 | 0 | Hydrophobic |
