The dishevelled (Dvl) PDZ domain is believed to play an essential role in the canonical and noncanonical Wnt signaling pathways, which are involved in embryo development as well as in tumorigenesis. Also, it binds directly to frizzled (Fz) receptors. An organic molecule (NSC668036) from the National Cancer Institute small-molecule library has been identified to be able to bind to the Dvl PDZ domain. Molecular dynamics simulation was used to provide detailed analyses of the binding between them.