Protoporphyrinogen oxidase (Protox) is the molecular target of a large number of herbicides. These herbicides compete with protoporphyrinogen IX (Protogen IX), the substrate of Protox, at or near the catalytic site on Protox. In this paper, taking Protogen IX as reference compound, eight of typical Protox inhibitors were superimposed to fit with their most favorite conformation to build Protox's pharmacophore model by using distance-comparisons (DISCO) method without the three-dimensional structure of Protox. Based on these, a probable active conformation of Protogen was conformed when the interaction occurred between the Protogen IX and Protox. All of these are useful clues for designing novel Protox inhibitors.

Key words: PROTOPORPHYRIN, OXIDASE, ENZYME INHIBITOR, HERBICIDES, CONFORMATION