X-ray crystallography studies as well as live-cell fluorescent imaging have recently challenged the traditional view of Protein-kinase CK2. Unbalanced expression of catalytic and regulatory CK2 subunits has been observed in a variety of tissues and tumors. Thus, the potential intersubunit flexibility suggested by these studies raises the likely prospect that the CK2 holoenzyme complex is subject to disassembly and re-assembly. In this study, we show evidence for the reversible multimeric organization of the CK2 holoenzyme complex in vitro. We used a combination of site-directed mutagenesis, binding experiments and functional assays to show that both in vitro and in vivo, only a small set of primary hydrophobic residues of CK2β which contacts at the center of the CK2α/CK2β interface dominates affinity. The results indicate that a double mutation in CK2β of amino acids - Y188 and F190 - which are complementary and fill up a hydrophobic pocket of CK2α is the most disruptive to CK2α binding both in vitro and in living cells. Further characterization of hot spots in a cluster of hydrophobic amino acids centered around Y188-F190 led us to the structure-based design of small peptide inhibitors. One conformationally constrained 11-mer peptide (Pc) represents a unique CK2β-based small molecule that was particularly efficient 1) to antagonize the interaction between the CK2 subunits, 2) to inhibit the assembly of the CK2 holoenzyme complex, 3) to strongly affect its substrate preference.