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Combinations of Protein-Chemical Complex Structures Reveal New Targets for Established Drugs

Figure 2

Examples from the benchmark dataset of high-quality predictions.

(A): High-identity subset: the complex of dihydrofolate reductase from Pneumocystis carinii with trimethoprim predicted using complexes with dihydrofolate reductase from Mycobacterium tuberculosis (with trimethoprim, PDB code 1DG5) and methotrexate (with dihydrofolate reductase from Pneumocystis carinii, 1DF7, with dihydrofolate reductase from Mycobacterium tuberculosis, PDB code 3CD2). RMSD from a known 3D structure (PDB code 1DYR) is 0.82 Å. (B): Low-identity or non-homology subset: the complex of endoplasmin GRP94 with radicicol using complexes with pyruvate dehydrogenase kinase isoform 3 (PDK3) (with radicicol, PDB code 2Q8I) and ATP (with PDK3, PDB 1Y8O, with CRP94, PDB 1TC6). RMSD from a known 3D structure (PDB 1QY8) is 0.87 Å.

Figure 2

doi: https://doi.org/10.1371/journal.pcbi.1002043.g002