A novel mixed-ligand zinc(II) complex with iminodiacetato(2-) (IDA) and adenine (AdeH) ligands has been obtained. Its crystal consists of octahedral molecules [Zn(IDA)(AdeH)(H2O)(2)] where the selective Zn-N9(AdeH) bond, involving the most basic N(AdeH) donor atom, occupies the trans position versus the Zn-N(IDA) bond. The Zn(II)-N9(AdeH) binding mode seems to be rare enough in comparison to those previously reported for Zn(II) and AdeH or a variety of related ligands. The chelate-nucleobase recognition process is further accomplished by an O-H(aqua)(...)N3(adenine) inter-ligand H-bonding interaction, without any intramolecular IDA-nucleobase interaction. This finding is attributed to the polarizing effect of Zn(II) on the aqua ligand and the possibilities of AdeH acting as N-donor for the metal(II) atom and H-acceptor for an intra-molecular inter-ligand H-bonding interaction. There are no aromatic pi,pi-stacking contributions in the 3D H-bonded network, where all polar N-H (IDA or AdeH) and O-H (aqua) bonds are involved as donors in H-bonding interactions, which include AdeH:AdeH and IDA:AdeH pairing by double inter-molecular bridges.