The synthesis of uracil derivatives and their conversion to a number of potential compounds have drawn attention of researchers aiming to develop innovative materials. Therefore, a novel azo ligand, 1,3-dimethyl-5-(5′-methyl-3′-isoxazolyl-azo)-6-aminouracil (H2L, 1), was synthesized from 1,3-dimethyl-6-aminouracil and 3-amino-5-methyl-isoxazole. Compound 1 was converted to an 8-azaxanthine derivative, 1,3-dimethyl-8-(5′-methyl-3′-isoxazolyl)azaxanthine (2), via its reaction with Cu(NO3)2·6H2O in DMF solution. Alternatively, when 1 reacted with Cu(CH3COO)2·H2O in the presence of NaN3in methanol, an antiferromagnetic Cu(ii) complex (3) was formed, where Cu(ii) is found to be coordinated with the in situ-generated novel ligand 1,3-dimethyl-5-(but-2-one-3-ene-4-amino-azo)-6-aminouracil (L1) and azide ions. The structures of these compounds (1–3) were characterized using single crystal X-ray analysis. Complex 3 is a tetrameric assembly of Cu(ii) with a nearly parallelogram shape. Its Cu(ii) centers are interconnected through doubly end-on azide (μ1,1-azide) bridges and doubly end-to-end azo (μ1,2-azo) bridges. The theoretical study shows the presence of non-covalent interactions, including H-bonding and stacking interactions. Magnetic studies of 3, a nearly parallelogram tetranuclear Cu(ii) unit with side lengths of 3.7839(6) Å and 4.7727(8) Å, revealed that it possesses strong antiferromagnetic interactions, as evidenced by its exchange coupling constant J1= −250 (1) cm−1through end-on azide bridging between the Cu(ii) ions (Cu–N–Cu, 116°). Thus, the present study not only introduces a strong antiferromagnetic material, but also establishes a notable correlation between its structure and magnetic properties.