A new series of pyrimidine derivatives was designed and synthesized from 2-thiouracil via multicomponent, Biginelli-type reactions and structurally characterized by all spectral means. Synthesized compounds were evaluated for antiproliferative activity against Ehrlich ascites tumour (EAT) cells. A molecular docking study was carried out to establish the binding mode of these compounds into human casein kinase-2 inhibitor (CK2). The established binding modes of these compounds into human CK2 were in very good agreement with the in vitro antiproliferative activity. Compound 4-(2-(1H-indol-2-yl)ethylamino)-2-(2-(diethylamino)ethylthio)-6-(4-fluorophenyl)pyrimidine-5-carbonitrile 4h exhibited stronger cytotoxic activity against EAT cells with an IC50 value of 5.2 μM which was the nearest cytotoxic activity compared with the standard drug methotrexate (MTX) that showed an IC50 value of 3.6 μM. Compound 4h has the maximum cytotoxicity against EAT cell, the lowest binding energy (-8.7 kcal/mol) and good ligand efficiency with CK2 compared to all other compounds. © 2015 Springer Science+Business Media Dordrecht.