The Leishmania protein target with the best overall docking properties with Copaifera diterpenoids was L. major dihydroorotate dehydrogenase (average Edock = −109.2 kJ/mol). These docking energies were better than the docking energy for the normal substrate, dihydroorotate (Edock = −72.1 kJ/mol) and comparable to the co-crystallized ligand for this protein, nitroorotate (Edock = −104.2 kJ/mol). Docking energies for Copaifera diterpenoids with TcDHODH (average −92.5 kJ/mol) were also better than the normal substrate (dihydroorotate, Edock = −64.2 kJ/mol), but worse than the synthetic TcDHODH inhibitor, 5-[2-(5-carboxynaphthalen-2-yl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydro-pyrimidine-4-carboxylic acid (TT2-2-199, Edock = −140.7 kJ/mol). Similarly, Copaifera diterpenoids docked with L. donovani DHODH (average Edock = −89.9 kJ/mol) better than dihydroorotate (Edock = −60.9 kJ/mol). Based on these docking energies, protozoal dihydroorotate dehydrogenases are likely targets for Copaifera diterpenoids.