Hidden-color configurations are a key prediction of QCD with important physical consequences. In this work we examine a QCD color-singlet configuration in nuclei formed by combining six scalar [ud] diquarks in a strongly bound SU(3)C channel. The resulting hexadiquark state is a charge-2, spin-0, baryon number-4, isospin-0, color-singlet state. It contributes to alpha clustering in light nuclei and to the additional binding energy not saturated by ordinary nuclear forces in He4 as well as the alpha-nuclei sequence of interest for nuclear astrophysics. We show that the strongly bound combination of six scalar isospin-0 [ud] diquarks within the nuclear wave function - relative to free nucleons - provides a natural explanation of the EMC effect measured by the CLAS collaboration's comparison of nuclear parton distribution function ratios for a large range of nuclei. These experiments confirmed that the EMC effect; i.e., the distortion of quark distributions within nuclei, is dominantly identified with the dynamics of neutron-proton (“isophobic”) short-range correlations within the nuclear wave function rather than proton-proton or neutron-neutron correlations.