Crystal engineering of nanoporous structures has not yet exploited the heme motif so widely found in proteins. Here, we report that a derivative of iron phthalocyanine, a close analog of heme, forms millimeter-scale molecular crystals that contain large interconnected voids (8 cubic nanometers), defined by a cubic assembly of six phthalocyanines. Rapid ligand exchange is achieved within these phthalocyanine nanoporous crystals by single-crystal-to-single-crystal (SCSC) transformations. Differentiation of the binding sites, similar to that which occurs in hemoproteins, is achieved so that monodentate ligands add preferentially to the axial binding site within the cubic assembly, whereas bidentate ligands selectively bind to the opposite axial site to link the cubic assemblies. These bidentate ligands act as molecular wall ties to prevent the collapse of the molecular crystal during the removal of solvent. The resulting crystals possess high surface areas (850 to 1000 square meters per gram) and bind N2 at the equivalent of the heme distal site through a SCSC process characterized by x-ray crystallography.