Two Mn(II) and Ni(II) coordination complexes viz. [Mn(phen)2(2,6-PDC)]·2CH3OH (1) and [Ni(2,6-PDC)2][Ni(H2O)4(en)]·6H2O (2) (phen = 1,10-phenanthroline, 2,6-PDC = 2,6-pyridinedicarboxylate and en = ethylenediamine) have been isolated at ambient conditions and characterized by elemental analysis, FT-IR, electronic spectroscopy, TGA and single crystal X-ray diffraction. Switching the solvent from methanol to water has changed the structural topologies of the compounds. Compound 1 is composed of a hepta-coordinated Mn(II) centre with two bidentate phen and one tridentate 2,6-PDC; whereas compound 2 is composed of cationic [Ni(H2O)4(en)]2+ and anionic [Ni(2,6-PDC)2]2– moieties with hexa-coordinated Ni(II) centers. Crystal structure analysis of compound 1 unfolds the presence of unorthodox OH(methanol)⋯π interactions involving the uncoordinated methanol molecules. The unusual enclathration of dual H-bonded guest (H2O)4 cores in the hexameric Ni(II) hosts in compound 2 provides rigidity to the crystal structure. The antiparallel π-stacked dimers and anti-cooperative HB···anion-π···HB assemblies observed in the solid-state structures of 1 and 2 respectively have been studied theoretically using DFT calculations and NCI plot index computational tools. In vitro anticancer evaluation of the compounds considering cell cytotoxicity and apoptosis assay showed significant concentration dependent cytotoxicity in Dalton’s lymphoma (DL) cancer cells with nominal effects in normal PBMC cells. To elucidate the possible mode of action of the cytotoxic behavior of the compounds, in silico docking studies have been carried out which revealed the efficient interaction of the compounds with the active sites of antiapototic cancer target proteins. The inhibitions of the activities of antiapoptotic target proteins have been further investigated using western blot analysis.