Analyzing Cyp3A4 PDB structures

An assessment of ligand density fit (real space correlation coefficient, RSCC, plus visual inspection of the density) across the 109 ligand-bound CYP3A4 structures in the PDB, with recommendations for which structures to exclude, or restrict to chain A, when using them to train or evaluate models. Structures with ligands in allosteric sites or in non-pharmacologically relevant conditions are also flagged for exclusion. Version 2 adds 8DYC (glycerol coordinating the heme) and the progesterone-bound structures 5A1P, 5A1R and 1W0F (allosteric site) to the exclusion list, and updates Fig 2 and the accompanying text. This is an archival copy (Markdown text plus figures) of an OpenADMET analysis write-up. All seven figures are static originals from the source document.