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The molecular and supramolecular structures of some M(II) complexes (M = Co, Mn, Cu, Ni, Zn) with a hydrazone-s-triazine ligand (BMPyTr) were discussed based on single crystal X-ray diffraction (SCXRD), Hirshfeld and DFT analyses. A new Co(II) complex of the same ligand was synthesized and its structure was confirmed to be [Co(BMPyTr)Cl2]·H2O based on FTIR and UV–Vis spectra, elemental analysis and SCXRD. The geometry around Co(II) was a distorted square pyramidal configuration (τ5 = 0.4), where Co(II) ion is coordinated to one NNN-tridentate ligand (BMPyTr) and two Cl- ions. A Hirshfeld analysis indicated all potential contacts within the crystal structure, where the percentages of O⋯H, N⋯H, C⋯H, and H⋯H contacts in one unit were 11.2, 9.3, 11.4, and 45.9%, respectively, while the respective values for the other complex unit were 10.3, 8.8, 10.6, and 48.0%. According to DFT calculations, the presence of strongly coordinating anions, such as Cl-, in addition to the large metal ion size, were found to be the main reasons for the small M-BMPyTr interaction energies in the cases of [Mn(BMPyTr)Cl2] (260.79 kcal/mol) and [Co(BMPyTr)Cl2]·H2O (307.46 kcal/mol) complexes. Interestingly, the Co(II) complex had potential activity against both Gram-positive (S. aureus and B. subtilis) and Gram-negative (E. coli and P. vulgaris) bacterial strains with inhibition zone diameters of 13, 15, 16, and 18 mm, respectively. Also, the new [Co(BMPyTr)Cl2]·H2O (IC50 = 131.2 ± 6.8 μM) complex had slightly better cytotoxic activity against HCT-116 cell line compared to BMPyTr (145.3 ± 7.1 μM).