Vesicular acetylcholine transporter (VAChT) is inhibited by (−)-vesamicol [(−)-trans-2-(4-phenylpiperidino)cyclohexanol], which binds tightly to an allosteric site. The tertiary alkylamine center in (−)-vesamicol is protonated and positively charged at acidic and neutral pH and unprotonated and uncharged at alkaline pH. Deprotonation of the amine has been taken to explain loss of (−)-vesamicol binding at alkaline pH. However, binding data deviate from a stereotypical bell shape, and more binding occurs than expected at alkaline pH. The current study characterizes the binding of (−)-vesamicol from pH 5 to pH 10 using filter assays, (−)-[ 3 H]vesamicol (hereafter called [ 3 H]vesamicol), and human VAChT expressed in PC12 A123.7 cells. At acidic pH, protons and [ 3 H] vesamicol compete for binding to VAChT. Pre-or long term-exposure of VAChT to high pH does not affect binding, thus eliminating potential denaturation of VAChT and failure of the filter assay. The dissociation constant for the complex between protonated [ 3 H]vesamicol and VAChT decreases from 12 nM at neutral pH to 2.1 nM at pH 10. The simplest model of VAChT that explains the behavior requires a proton at Site 1 to dissociate with pK 1 = 6.5 ± 0.1, a proton at Site A to dissociate with pK A = 7.6 ± 0.2, and a proton at Site B to dissociate with pK B = 10.0 ± 0.1. Deprotonation of the Site 1 proton is obligatory for [ 3 H]vesamicol binding. Deprotonation of Site A decreases affinity (2.2 ± 0.5)-fold and deprotonation of Site B increases affinity (18 ± 4)-fold. Time-dependent dissociation of bound [ 3 H]vesamicol is biphasic, but equilibrium saturation curves are not. The contrasting phasicity suggests that the pathway to and from the [ 3 H]vesamicol binding site exists in open and at least partially closed states. The potential significance of the findings to development of PET and SPECT ligands based on (−)-vesamicol for human diagnostics also is discussed.Vesicular acetylcholine transporter (VAChT 1 ) moves the neurotransmitter acetylcholine (ACh) from the cytoplasm of nerve terminals to the inside of synaptic vesicles (1,2). It belongs to the major facilitator superfamily (MFS) of transporters, most of which contain twelve transmembrane (TM) helices (3). Three-dimensional structures for four bacterial members of the MFS have been determined. They are lactose permease (4), glycerol phosphate transporter (5), oxalate-formate antiporter (6), and the multidrug resistance transporter EmrD (7). The structures all exhibit similar TM nearest neighbors (4,5,6). The first six TMs in the amino acid sequence pack into one bundle, and the second TMs pack into another bundle. The bundles are † This research was supported by Grant NS15047 from the National Institute of Neurological Disorders and Stroke. *To whom correspondence should be addressed: Department of Chemistry and Biochemistry, University of California, Santa Barbara, 893-2252. Fax: (805) 893-4120.. 1 Abbreviations: (±)-ABV, (±)-aminobenzovesamicol; ACh, acetylcholine; AMPSO, (N-(1,1-dimethy...