By definition, the concept of a dielectric constant is used to describe the collective behavior of matter and does not describe effects on the atomic level. In practice, using low dielectric constants for the solute (protein), such as =2, accounts for electronic polarizability and is more sensitive to changes in the molecules, and can therefore be very useful for distinguishing between rather similar ligands. Nonetheless, as we point out with this study, the standard employment of such low dielectric constants may lead to wrong assumptions on the relative ranking of ligands, particularly when they differ in charges. Special care needs to be taken to adjust the dielectric constant for the system under investigation in order to avoid artefacts (e.g. contributions from polar residues located far from the binding site). Based on this study we suggest the use of a rather elevated solute dielectric constant of about 8 for kinases, in particular when investigating charged ligands.