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Structural comparison of ‘Public Baseline’ AML to clinical-stage therapeutics.

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posted on 2021-03-01, 18:40 authored by Matthew I. J. Raybould, Claire Marks, Aleksandr Kovaltsuk, Alan P. Lewis, Jiye Shi, Charlotte M. Deane

The eleven clinical-stage therapeutic antibodies with a solved crystal structure within 0.75Å variable domain (Fv) root-mean-squared deviation (RMSD) of an antibody model structure from the Public Baseline Antibody Model Library (PB AML). The first column records the Fv identifier for the geometrically closest AML model to each of the eleven therapeutics listed in column 2. Column 3 provides the Protein Data Bank (PDB) identifier for each chosen therapeutic structure (chain identifiers in brackets). The corresponding RMSD is provided in column 4; all RMSD comparisons were made between AML structures and therapeutics with an identical combination of CDR lengths. This combination of North-defined CDR lengths is then listed in the order H1-H2-H3-L1-L2-L3. Finally, the target for each therapeutic antibody is recorded. PDB = Protein Data Bank; VH = variable heavy chain; VL = variable light chain; Fv = Fragment variable region; RMSD = root-mean-squared deviation; CDR = Complementarity-Determining Region. Antigens: CD—Cluster of Differentiation protein, NGFB—Nerve Growth Factor B, IL—interleukin, TSLP—Thymic Stromal Lymphopoietin, APP—Amyloid Precursor Protein, MIF—Macrophage Migration Inhibitory Factor, IGHE—Immunoglobulin Heavy Constant Epsilon.