Proton decay is one of possible signatures of baryon number violation, which has to exist to explain the baryon asymmetry and the existence of nuclear matter. Proton decays must be mediated through effective low-energy baryon number violating operators made of three quarks and a lepton. We calculate matrix elements of these operators between the proton and various meson final states using the direct method. We report on preliminary results of matrix element calculation done with the 2+1 dynamical flavor domain wall fermions at the physical point for the first time.