The structural diversity of natural sulfated glycosaminoglycans (GAGs) presents major promise for discovery of chemical biology tools or therapeutic agents. Yet, few GAGs have been identified so far to exhibit this promise. We reasoned that a simple approach to identify such GAGs is to explore sequences containing rare residues, for example, 2-O-sulfonated glucuronic acid (GlcAp2S). Genetic algorithm-based computational docking and filtering suggested that GlcAp2S containing heparan sulfate (HS) may exhibit highly selective recognition of antithrombin, a key plasma clot regulator. HS containing only GlcAp2S and 2-N-sulfonated glucosamine residues, labeled as HS 2S2S , was chemoenzymatically synthesized in just two steps and was found to preferentially bind antithrombin over heparin cofactor II, a closely related serpin. Likewise, HS 2S2S directly inhibited thrombin but not factor Xa, a closely related protease. The results show that a HS containing rare GlcAp2S residues exhibits the unusual property of selective antithrombin activation and direct thrombin inhibition. More importantly, HS 2S2S is also the first molecule to activate antithrombin nearly as well as the heparin pentasaccharide although being completely devoid of the critical 3-O-sulfonate group. Thus, this work shows that novel functions and mechanisms may be uncovered by studying rare GAG residues/sequences. S ulfated glycosaminoglycans (GAGs), natural linear copolymers of hexuronic acid and hexosamine residues, represent nature's bounty of chemical biology tools and therapeutic agents. Despite this, the current state-of-art displays minimal exploitation of this promise. Few GAG-based agents have been used to elucidate new pathways and very few GAG-based agents, other than polymeric heparin and dermatan sulfate, have reached the clinic. A major challenge in realizing the true biochemical and pharmacologic potential of GAGs is the structural microheterogeneity present in the GAGs isolated from tissues or cells. The variations introduced by nontemplate-driven sulfation, deacetylation, and epimerization reactions during their biosynthesis, 1,2 coupled with the postsynthetic fine-tuning of their structure by sulfatases, 3 generate millions of distinct sequences that pose significant challenges for detailed structural analysis.Despite these challenges, sulfated GAGs are very attractive as potential seeds for new drugs. The presence of O-sulfonate ( OSO 3¯) groups on a GAG chain induces recognition and modulation of most proteins, especially those that display a collection of arginine and lysine residues on their surface. This gives rise to GAG modulation of a large number of physiological and pathological responses such as growth and cancer, cell renewal and differentiation, hemostasis and fibrinolysis, inflammation and immune response, and microbial invasion and defense. 2 It is likely that individual proteins bind to only a subset of GAG sequences from the natural repertoire of millions. A classic example of this high selectivity is the heparin pentasa...