The DNA binding and the antibacterial activities of metal organic compounds have great significance for the development of anticancer drugs. In this study, a copper coordination network, [Cu2L(H2O)2]n (CuNet), based on H4L where 2,6-pyridine-dicarboxylic acid moieties are spaced by p-benzyloxy, is prepared hydrothermally. Single crystal X-ray analysis demonstrates that the fully deprotonated ligand L4– with high planarity in CuNet adopts a bis-µ2-η1: η1: η2 coordination mode to bind four Cu(II) to render a graphene-like network, which is further propped up to a 3D supramolecular framework through the hydrogen bonds between coordinated water and uncoordinated carboxyl oxygen. Considering its highly planar structural feature and excellent antibacterial properties of Cu(II), the DNA binding and antibacterial performance were explored. The UV-Visible absorption titration and EB-DNA competition determination exhibited that CuNet bound DNA in an intercalation mode with the higher binding constant Kb of 2.42 × 105 M− 1, and the comparable quenching constant Ksv of 1.62 × 104 M− 1 upon compared with the documented DNA linkers. In addition, the antibacterial activity test demonstrates that CuNet exhibits comparable inhibitory effect on Escherichia coli with that of cefradine at the concertation of 0.70 mg/mL. This work has certain significance for the development of metal drugs.