In an attempt to discover more potent ligands, we present here a docking study for ionotropic glutamate receptor subtype 6 which is important in many neurodegenerative diseases. Total 97 compounds including a small series of commercially available compounds are characterized in iGluR6 binding. Z-scores were employed to recognize hits for this receptor. Twenty eight compounds were shown to have excellent binding affinity on this target. A detailed in silico study showed the strong interactions of compound no. 2h and 13515655 with iGluR6. Total four anchors were found. They involve three hydrogen bonding interactions and one vander waal interaction.