Introduction: Worldwide, breast cancer is the most life-threatening disease among women. There is always high search to find a cure for cancer. Plant compounds have been identified that they have anti-cancer properties. Therefore, phyto-compounds can be potential for the development of new drugs. In this research, three-dimensional (3D) structure of breast cancer cell line proteins, tumor suppressor gene (p53), caspase-3 and retinoblastoma-1 were generated and docking with plant compounds (garcinone E, triterpenoid and gallic acid respectively) was studied. Methods: The three-dimensional models of proteins were built using SWISS model. Then, the physical and chemical characters of the protein models were determined using ExPASy - ProtParam tool. Next, the proteins were assessed using validation tools such as PROCHECK, ProQ, ERRAT and Verify 3D programs. Results: The results show that the proteins were stable. Lastly, the protein models were docked successfully with garcinone E, triterpenoid and gallic acid respectively using BSP-slim server. The docking scores of the protein-phyto-compound complexes (p53-garcinone E, caspase-3- triterpenoid and Rb1-gallic acid) were 3.873, 4.321 and 3.051 respectively. The proteins had a stable bond with phyto-compounds. Conclusion: The study of the protein-phyto-compound complex interaction will aid in designing new clinical drugs.