Intermetallics contribute significantly to our current demand for high-performance functional materials. However, understanding their chemistry is still an open and debated topic, especially for complex compounds such as approximants and quasicrystals. In this work, targeted topological data mining succeeded in (i) selecting all known Mackay-type approximants, (ii) uncovering the most important geometrical and chemical factors involved in their formation, and (iii) guiding the experimental work to obtain a new binary Sc–Pd 1/1 approximant for icosahedral quasicrystals containing the desired cluster. Single-crystal X-ray diffraction data analysis supplemented by electron density reconstruction using the maximum entropy method, showed fine structural peculiarities, that is, smeared electron densities in correspondence to some crystallographic sites. These characteristics have been studied through a comprehensive density functional theory modeling based on the combination of point defects such as vacancies a...