The problem of deriving a gradient flow structure for the porous medium equation which is {\em thermodynamic}, in that it arises from the large deviations of some microscopic particle system, is studied. To this end, a rescaled zero-range process with jump rate $g(k)=k^α, α>1$ is considered, and its hydrodynamic limit and dynamical large deviations are shown in the presence of both degenerate and unbounded diffusion. The key superexponential estimate is obtained using pathwise discretised regularity estimates in the spirit of the Aubin-Lions-Simons lemma. This allows to exhibit the porous medium equation as the gradient flow of the entropy in a thermodynamic metric via the energy-dissipation inequality.