Adenosine is an endogenous modulator exerting its functions through the activation of four adenosine receptor (AR) subtypes, termed A 1, A 2A, A 2B and A 3, which belong to the G-protein-coupled receptor superfamily. The human A 3AR (hA 3AR) subtype is implicated in several cytoprotective functions. Therefore, hA 3AR modulators, and in particular agonists, are sought for their potential application as anti-inflammatory, anti-cancer and cardioprotective agents. Here, we prepared novel adenosine derivatives with indole moiety as hA 3AR ligands. According to the biological assay, we found that 2-substituents 11 were critical structural determinants for A 3AR ligands ( K i = 111 nM). The observed structure–affinity relationships of this class of ligands were also exhaustively rationalized using the molecular modelling approach. This allows the investigation on the binding mode of the potential compound in the ligand-binding pocket of the human A 3 receptor. The results demonstrated that 11 can interact with the ASN250, GLN167, PHE168 and VAL178 through hydrogen bonding, which are shown to be important for ligand–receptor interaction.