Recently, a GPU-accelerated and purely LB approach based on numerical collision was proposed and validated in two dimensions. The model showcased features such as variable Prandtl number, inclusion of forcing terms in moment space and increased stability in under resolved conditions, when compared to its parent model of Numerical Equilibrium. The proposed approach was also shown to seamlessly run on CPUs or GPUs thanks to the recent upgrade of the C++ STL library and NVIDIA compiler. In this work we showcase the viability of numerical collision model in a three-dimensional context. We use the combination D3Q39 lattice and 13-moment (3D) model to move to 3D, and validate using an extensive suite of test cases which includes sod shock-tube, double-shear layer, Taylor-Green vortex and supersonic flow past spherical geometry. We confirm the feasibility of the proposed method in a variety of compressible flow configurations, by comparing results against analytical and experimental solutions available in literature.