Contemporary drug design projects frequently mix and match chemical structures with biochemical building blocks such as peptides and nucleotides, both natural and unnatural. Druggable targets are often hypothesized as various flavors of peptides, RNA and DNA. The line between ligand and receptor can be blurred, with complex entities like antibody drug conjugates or functionalized oligonucleotides as either therapeutic agents or targets. One of the rate limiting steps to discovery is the ability to represent all of these kinds of molecular entities for registration purposes. Checking for duplicates, calculations and searches based on chemical structures, and bioinformatics operations using sequences of natural analogs are all essential core functionality. We will discuss how we have leveraged V3000 templates to represent conjugate macromolecules in a sketch-like format, used mixture containers to associate non-stoichiometric components, and added custom registration fields to capture metadata for classification purposes, all within the framework of CDD Vault.