Niemann-Pick C1-like protein (NPC1L1) mediates the absorption of dietary cholesterol in the proximal region of the intestine, a process that is blocked by cholesterol absorption inhibitors (CAIs), including ezetimibe (EZE). Using a proteomic approach, we demonstrate that NPC1L1 is the protein to which EZE and its analogs bind. Next, we determined the site of interaction of EZE analogs with NPC1L1 by exploiting the different binding affinities of mouse and dog NPC1L1 for the radioligand analog of EZE, [ 3 H]AS. Chimeric and mutational studies indicate that high-affinity binding of W hole-body cholesterol homeostasis is maintained through three major pathways: de novo synthesis, intestinal absorption, and biliary excretion. Absorption of dietary and biliary cholesterol occurs in the proximal jejunum of the small intestine (1), and this process is blocked by ezetimibe (EZE), a drug used for the treatment of hypercholesterolemia. EZE, a potent cholesterol and phytosterol uptake inhibitor, effectively lowers circulating plasma cholesterol in humans by 15-20% (2), and its coadministration with 3-hydroxy-3-methylglutaryl CoA (HMG CoA) reductase inhibitors (statins), inhibitors of cholesterol synthesis, leads to further reductions in cholesterol plasma levels (3).By searching expressed sequence tag databases for the presence of a sterol-sensing domain (SSD), a plasma membrane secretion signal, and enriched expression in intestinal enterocytes, the Niemann-Pick C1-Like 1 (NPC1L1) protein was identified in 2004 as a potential candidate gene for the EZE-sensitive pathway of cholesterol absorption (4). Mice deficient in NPC1L1 were found to have Ϸ70% reduction in sterol absorption, with the residual component being insensitive to EZE (4), suggesting that NPC1L1 is a critical component of cholesterol uptake in enterocytes (4). The use of enterocyte brush border membranes (BBMs) from several species, including NPC1L1 KO mice (5), or membranes derived from cells expressing recombinant NPC1L1, has provided strong evidence for NPC1L1 being the target to which EZE binds (5).More recently, in vitro studies have demonstrated EZE-sensitive cholesterol transport into McArdles RH7777 hepatoma (6), CaCo-2 (7), and MDCKII cells (8) overexpressing NPC1L1. However, although EZE-sensitive cholesterol transport correlates well with the amount of NPC1L1 expression (7, 8), it is not possible to determine whether NPC1L1 functions alone or as part of a multiprotein complex [SR-B1 (9-15), CD36 (14), CD13 (9), caveolin-1/annexin-2 (16)], facilitating the transfer of cholesterol from outside the cell to internal cholesterol pools (9, 15). Furthermore, it has been speculated that EZE may inhibit cholesterol transfer by binding to some of these other targets, in addition to its inhibition of NPC1L1 (9).In the present study, we attempted to determine whether EZE binds to NPC1L1 directly by purifying an EZE-NPC1L1 complex and analyzing its constituents by mass spectrometry. Quantitative analysis unambiguously demonstrated that NPC1L1 is the only prote...