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. Author manuscript; available in PMC: 2008 Aug 15.
Published in final edited form as: J Med Chem. 2006 Jun 15;49(12):3553–3562. doi: 10.1021/jm060092o

Figure 5. Specificity of GAG sequence for antithrombin.

Figure 5

Variation in the RMSD between six solutions (1, 1′, 2, 2′, 3, and 3′) obtained from three independent docking experiments of heparin pentasaccharide H5 variants, containing either one additional sulfate group at 3-position of residue E or lacking a sulfate at the 3-position of residue F, binding to antithrombin. Whereas for H5 (A) the RMSD was less than 2.0 Å between each solution, for H5-3SF (B) and H5+3SE (C), a majority of RMSD values were much greater (5-17 Å). Other pentasaccharide variants were also studied. See text for details.