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Figure 7
Idealized and example coordinates for the PDBCCD entry IDS (2-O-sulfo α-L-iduronic acid) and their comparison with a minimal energy conformer calculated by torsional exploration and minimization with RDKit. The blue area denotes those atoms which lie roughly in a plane, making it easier to identify the ring conformation. Top, the biologically relevant 1C4 conformer, as stored in the PDBCCD idealized coordinates. Despite showing repulsion between axial substituents, this chair conformation is the only feasible conformation, as converting it into the slightly more favourable 4C1 chair would require a considerable energetic investment. Middle, example coordinates as determined by NMR (Mulloy et al., 1993BB71). This conformer is in a high-energy conformation and does not match any of the available high-resolution crystallographic structures. Bottom, a 4C1 chair conformer obtained by torsional exploration with RDKit (Landrum, 2016BB49). The aforementioned energy barrier is artificially circumvented by exploring different combinations of torsions. This is the absolute minimal energy conformation, but one that is not attainable without external intervention. This figure was generated with CCP4mg (McNicholas et al., 2011BB65).

Journal logoSTRUCTURAL
ISSN: 2059-7983
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