HIV-1 reverse transcriptase (RT) — which plays an essential role in the virus life cycle — is the target of two classes of approved anti-HIV drugs. Now, La et al. use a combination of saturation-transfer difference (STD) NMR and in vitro activity assays to screen a library of fragment-sized compounds with the aim of identifying new drug scaffolds targeting HIV-1 RT. Three compounds were found to potently inhibit HIV-1 RT in cell culture, including RT variants displaying resistance to existing clinical inhibitors. Importantly, two of the compounds have mechanisms distinct from those of existing agents, competitively inhibiting HIV-1 RT with respect to the dNTP substrate or the DNA template or primer.