The structure of crystalline nanoparticles (CNPs) is determined using dynamic nuclear polarization (DNP) enhanced NMR spectroscopy experiments. The CNPs are composed of a crystalline core containing an active pharmaceutical ingredient (compound P), coated with a layer of PEG (DSPE-PEG 5000) located at the crystal surface, in a D2O suspension. Relayed DNP experiments are performed to study 1H-1H spin diffusion and to determine the size of the crystalline core as well as the thickness of the PEG overlayer. This is achieved through selective doping to create a heterogeneous system in which the D2O contains glycerol and organic radicals, which act as polarization sources, and the CNPs are exempt of radical molecules. We observe features that are characteristic of a core-shell system: high and constant DNP enhancement for components located in the surrounding radical solution, short build-up times for the PEG layer, and longer build-up times and time dependent enhancements for compound P. By comparing numerical simulations and experimental data, we propose a structural model for the CNPs with a core-shell organization and a high affinity between the radical and the PEG molecules.