We build a realistic E6 superstring inspired model with intermediate mass scales, which has the characteristic feature of containing no extra U(1) factors in the low energy scenario. This may be acquired starting from a suitable Calabi-Yau compactification with b1.1>1, such to give rise, after Hosotani breaking, to the rank r=5 gauge group SU (3)C× SU (2)L×U(1)Y× U (1)E, that is broken at an intermediate mass scale down to the standard model group. The minimization of the low energy effective potential and the renormalization group analysis are quantitatively performed, yielding viable mass spectra.