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. Author manuscript; available in PMC: 2014 Jun 27.
Published in final edited form as: J Med Chem. 2013 Jun 11;56(12):10.1021/jm4002988. doi: 10.1021/jm4002988

Figure 2.

Figure 2

MiniCD4 13 binds at the CD4-binding surface and extends into the gp120 Phe43 cavity. (A) gp120 is shown in grey surface representation with the CD4 binding footprint colored yellow. Knottin 13 is depicted in cartoon representation with the miniprotein colored red except residue 23, which is colored by element type with the nitrogen atoms colored blue and the carbon atoms of one conformation colored orange and the other magenta. (B) A cross-section of gp120 showing the side chain of residue 23 of peptide 13 penetrating the gp120 Phe43 cavity, packing coefficients and surface complementarity for each alternate conformation. Packing Coefficient (%) = (Volume of ligand/Volume of binding pocket) × 100. The colored dots span the region of the ligand used for each calculation.