Extended Data Fig. 5: Structural analysis of the ATX- and DSP-bound NET.

a, A comparative binding analysis between NET-ATX and dDAT-RTX. Left panel: Reboxetine in dDAT are colored light gray. The ethoxy group of reboxetine interacts with Ala117 and Phe325 of the dDAT structure, mirroring the placement of atomoxetine’s methyl group in NET. Right panel: Overlay of dDAT and NET shows a subtle backbone shift in residues 322–325 and the unique role of Pro323. b, A comparative binding analysis between NET-ATX and hDAT. Predicted human DAT structure are colored light gray. The predicted AlphaFold2 structure of DAT exhibits similarities to the NET structure with notable substitutions. Ser149 replaces Ala145, and Val324 replaces Ala321. The larger side chain of Val324 may cause a backbone shift of residues 323–326 towards the central pocket by steric effect. c-d, Distinct binding modes of desipramine or its analogs nortriptyline. Upper panel c: Desipramine binds within the central pocket of NET in an inward-open state. Lower panel c: In the inward-occluded LeuT structure, desipramine binds to an allosteric site distinct from the central pocket where leucine and two sodium ions bind. Panel d: Nortriptyline, an analog of desipramine, binds to the central pocket of dDAT in an outward-open state. Its orientation differs from that of desipramine in NET. e, The potential inhibitory mechanism of desipramine on NET. The first DSP binding site is the NTL binding site in the dDAT-NTL of the outward-open conformation; the second one is the DSP binding site in the LeuT-DSP of the occluded conformation; the third one is the DSP binding site in the NET-DSP of the inward-open conformation; and the last one is the DSP-2 binding site in the NET-DSP-KCl. Four distinct desipramine binding sites are marked with different colors: rose red, light blue, orange, and green. The dashed blue line symbolizes a potential transport pathway for desipramine within NET.