Objective: To analyze the interactions between clobazam and the benzodiazepine binding site, with focus on subtype-dependent interactions with the α-subunit subtypes. Background Clobazam, a 1,5-benzodiazepine, is in FDA review for Lennox-Gastaut syndrome. Design/Methods: To better understand the observed clinical profile of clobazam, we first characterized its GABA A -receptor-subtype–dependent positive allosteric modulation. Both clobazam and N-CLB were determined to be positive modulators. The benzodiazepine binding site was studied in a homology model. The primary template employed in the homology model was the X-ray structure of the glutamate-gated chloride channel from C. elegans. 1 Interaction patterns were analyzed through a pharmacophore model based on the consensus approach published by Cook and colleagues. 2 The pharmacophore model was extended to summarize the published structure-activity data for benzodiazepines exhibiting subtype-dependent binding to GABA receptors. Results: The homology model provides a suggested binding mode of clobazam consistent with published mutation data. Analysis indicates that there are only very few unconserved residues in the binding site. However, a less conserved part of the sequence forms the basis of a loop (the C-loop), which is important for the size and shape of the binding site. Results from the homology and pharmacophore models were consistent and further strengthen the hypothesis of which regions are most important for subtype-dependent binding — the pocket occupied by the 7-substituent and probably the 1,5-motif interacting with both the α- and the γ-subunits. Conclusions: Subtype-dependent differences in clobazam binding to the benzodiazepine site are indicated not as a result of unconserved residues in the core binding site, but rather as a result of less-conserved parts of the sequence that lead to different positions and dynamics of important loops in the binding site region. 1 Hibbs RE, et al. Nature . 2011;474:54–60. 2 Clayton T, et al. Curr Med Chem . 2007;14:2755–75. Supported by: H. Lundbeck A/S. Disclosure: Dr. Techau Bruun has received personal compensation for activities with Lundbeck Research USA, Inc. as an employee. Dr. Sindal Jensen has received personal compensation for activities with H. Lundbeck A/S as an employee. Dr. Ebert has received personal compensation for activities with Lundbeck Research USA as an employee.