Three coordination compounds, [Pb(pydc)]n (1), [Ca2(pydc)2(H2O)6]·2pydcH2 (2), and [ampyH]2[Ni(H2O)6][Ni(pydc)2]2·2H2O (3) (pydc = pyridine-2,6-dicarboxylate ion and ampy = 2-amino-4-methylpyridine), have been prepared by the hydrothermal method and characterized by elemental analyses, FTIR, 1H NMR spectroscopies, and single crystal X-ray diffraction. In 1 the connection of Pb(II) atom and pydc in a double-bridge and double-chelation coordination mode creates a layer structure extending in [202¯] plane, there is a π–π stacking interaction between these layers with a short face-to-face distance of 3.289 Å. Compound 2 consists of two pydcH2 molecules and a binuclear calcium(II) complex formed by the single-bridge and double-chelation coordination of pydc ligand. Compound 3 consists of two coordination anions [Ni(pydc)2]2−, one coordination cation, [Ni(H2O)6]2+, two protonated organic cations, ampyH+, and two water molecules. In [Ni(pydc)2]2−, Ni1 is coordinated by two (pydc)2− ligands in a double-chelate mode, exhibiting an octahedral geometry. The π–π stacking interactions between pydcH2 and the Ca complex in 2 and between pydc ligands in 3, and also the hydrogen bonds between coordination water molecules and pydcH2/pydc are the 3D supramolecular architecture constructing force. The protonation constants of ampy, pz (pyrazine) and pydcH2, as the building blocks of the proton transfer systems (pydcH2–ampy and pydcH2–pz) and their corresponding stability constants were determined by potentiometric studies. The stoichiometry and stability constants of pydc–ampy complex with Ni2+ and pydc–pz complexes with Ca2+ and Pb2+ was investigated by potentiometric technique in aqueous solution. The results from solution studies were compared with the solid state data, in details.