Bispyridinium cyclophanes are novel templates for human choline kinase inhibitors. Molecular modelling of these compounds suggests three anchorage places at the binding site of the enzyme: (i) two anionic centres of the enzyme active site separated from each other at a distance of approximately 6.2 A that bind the two positively charged nitrogen atoms; (ii) a wide hydrophobic pocket that is fulfilled by the upper linker, the benzene ring that links the two amino groups; and (iii) a smaller hydrophobic pocket that can accommodate the lower benzene ring that links both benzylic carbons. This study may be useful for the development of more potent inhibitors of the enzyme.