The present invention provides compositions and crystals of the carboxyltransferase (CT) domain (the C-terminal ˜90 kDa fragment) of various acetyl-CoA carboxylase (ACC) proteins, including yeast, mouse and human ACCs. Further, the present invention provides methods for identifying and designing compounds that can modulate ACC activity. These methods are based, in part, on the X-ray crystallographic structures of the CT domain of yeast ACC, either alone or bound to acetyl-CoA or a CT inhibitor, such as haloxyfop or diclofop or CP-640186. Thus, the present invention relates to the crystal structures of the carboxyltransferase (“CT”) domain of acetyl-CoA carboxylase (“ACC”), and to the use of these structures in the design of anti-obesity compounds, anti-diabetes compounds, antibiotic compounds, herbicide compounds, and in the design of herbicide resistant plants.