Two water-soluble copper(II) complexes of 6-(pyrazin-2-yl)-1,3,5-triazine-2,4-diamine (pzta) and amino acids, [Cu(pzta)(L-ArgH)(H(2)O)](ClO(4))(2) (1) and [Cu(pzta)(L-Met)(H(2)O)]ClO(4)·3H(2)O (2) (L-ArgH: protonated L-Argininate; L-Met: L-Methioninate), were synthesized and characterized. The determined X-ray crystallographic structures of 1 and 2 exhibited distorted square-pyramidal coordination geometries. Their binding properties toward calf thymus DNA (CT-DNA) and human serum protein (HSA) were measured by spectroscopic (UV-Vis, fluorescence, circular dichroism (CD)), calorimetric (isothermal titration calorimetry (ITC)) and molecular docking technology. DNA binding experiments showed that the complexes bound to DNA through a groove binding mode, the positive ΔH and ΔS values indicated that the hydrophobic interaction was the main force in the binding between the complexes and DNA. Besides, the complexes caused the fluorescence quenching of HSA through a static quenching procedure, changed the secondary structure and microenvironment of the Trp-214 residue, and preferably bound to subdomain IIA of HSA driven by hydrophobic and hydrogen-bond interactions. These results were further verified by the molecular docking technology. Furthermore, the in vitro cytotoxicities of the complexes against three human carcinoma cell lines (A549, PC-3 and HeLa) were evaluated, which confirmed that the complexation improved the anticancer activity of the pzta ligand significantly.