Abstract Set1C is a histone methyltransferase playing an important role in yeast gene regulation. Modeling the structure of this eight‐subunit protein complex is an important open problem to further elucidate its functional mechanism. Recently, there has been progress in modeling of larger complexes using constraints to restrict the combinatorial explosion in binary docking of subunits. Here, we model the subunits of Set1C and develop a constraint‐based docking approach, which uses high‐quality protein interaction as well as functional data to guide and constrain the combinatorial assembly procedure. We obtained 22 final models. The core complex consisting of the subunits Set1, Bre2, Sdc1 and Swd2 is conformationally conserved in over half of the models, thus, giving high confidence. We characterize these high‐confidence and the lower confidence interfaces and discuss implications for the function of Set1C.