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Earlier (Kireeva et al. Mol. Inf. 2012, 31, 301-312), we demonstrated that generative topographic mapping (GTM) can be efficiently used both for data visualization and building of classification models in the initial D-dimensional space of molecular descriptors. Here, we describe the modeling in two-dimensional latent space for the four classes of the BioPharmaceutics Drug Disposition Classification System (BDDCS) involving VolSurf descriptors. Three new definitions of the applicability domain (AD) of models have been suggested: one class-independent AD which considers the GTM likelihood and two class-dependent ADs considering respectively, either the predominant class in a given node of the map or informational entropy. The class entropy AD was found to be the most efficient for the BDDCS modeling. The predominant class AD can be directly visualized on GTM maps, which helps the interpretation of the model.