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Background: Colony morphology of embryonic stem (ES) cells contributes to the maintenance of undifferentiated ES cells. Small molecule 3,4-dihydropy-rimido[4,5-d]pyrimidine (SC1), an inhibitor of ERK1- and RasGAP-dependent signaling pathways, can maintain the compact colony morphology of ES cells. However, information on the influence of SC1 on cell morphological change remains lacking. Methods: In this study, mouse ES cells J1 and embryonic carcinoma (EC) cells F9 were cultured in SC1-containing medium to determine the effect of SC1 on cell morphology. Results: SC1 promotes a more compact morphology of J1 mouse ES cells and induces colony growth of F9 EC cells. Furthermore, the cell adhesion protein E-cadherin is a downstream target of SC1, and E-cadherin is critical for SC1-mediated colony growth of F9 EC cells. Conclusions: SC1 maintains and induces compact colony morphology of pluripotent cells, and its downstream target, E-cadherin, is involved in the colony phenotype of F9 EC cells. These results explored the potential role of SC1 in morphological change and gene expression in pluripotent cells.