Autodisplay was used for the co-display of GluN1 and GluN2A ligand binding domains (LBDs) of the N‑methyl-D-aspartate (NMDA) receptor in E. coli. LBDs were confirmed to be located at the cell surface and form dimers, similar to local LBD heterodimers present in full-length NMDA receptors. Flow cytometry was used to evaluate binding of fluorescently labeled TCN‑201 derivatives to cells with co-displayed LBDs. TCN-201 is a negative allosteric modulator of GluN2A containing NMDA receptors that binds at the LBD heterodimer interface of GluN1 und GluN2A. Among three TCN-201 derivatives, compound 8 was identified as a novel ligand that bound to cells co-displaying both LBDs but not to cells displaying exclusively one type of LBDs. This was to indicate that compound 8 addressed the same binding site as TCN-201. An apparent dissociation constant of 6.8 ± 1.6 µM for compound 8 was determined. Two-electrode voltage-clamp experiments showed that compound 8 did not inhibit GluN1/GluN2A NMDA receptor-mediated currents. However, compound 8 abolished the current inhibition by TCN-201, indicating competitive binding to the same binding site. Subunit selectivity of compound 8 was evaluated by fluorescence staining of recombinant NMDA receptors in mouse L(tk-) cells. Here, selective staining of GluN2A in contrast to GluN2B containing NMDA receptors with compound 8 was confirmed. Additionally, staining was prevented by preincubation with TCN-201, once more reaffirming the competitive binding mode. This work describes the identification of compound 8 which appears to be the first fluorescent small molecule labeling compound that selectively addresses GluN2A containing NMDA receptors.