Chemical space of molecules is a multi-dimensional space in which the alike molecules are grouped together based on their similarities. The chemical space terminology is commonly used in two distinct, yet related, concepts. First, it denotes the property space of an unknown size, which is spanned by all molecules that exist or are likely to exist. Secondly, it also finds use in the context of a given molecular dataset with a finite size. In the current study, we refer to the latter terminology of chemical space and focus on quantifying the similarities of molecules within domain-specific datasets.