Substrate Binding and Inhibition of the Anion Exchanger 1 Transporter Abstract: Anion Exchanger 1 (AE1), a member of the Solute Carrier (SLC) family, is the primary bicarbonate transporter in erythrocytes, regulating pH levels and CO2 transport between lungs and tissues. Previous studies characterised its role in erythrocyte structure, and provided insight into transport regulation. However, key questions remain regarding substrate binding and transport, mechanisms of drug inhibition, and modulation by membrane components. Here we present seven cryo-EM structures in apo, bicarbonate-, and inhibitor-bound states. These, combined with uptake and computational studies, reveal important molecular features of substrate recognition and transport, and illuminate sterol binding sites, to elucidate distinct inhibitory mechanisms of research chemicals and prescription drugs. We further probe the substrate binding site via structure-based ligand screening, identifying a AE1-inhibitor. Together, our findings provide insight into mechanisms of SLC transport and inhibition.