Fig. 3: Cheminformatic analyses of the pseudo-natural product collection.

a Principal moments of inertia (PMI) plot of the shape of the pseudo-natural product (PNP) collection (244 compounds, blue circles), chromane NPs (15 compounds, orange squares), indole NPs (15 compounds, green triangles), chromane/chromene synthetic compounds (15 compounds, red crosses), and indole synthetic compounds (15 compounds, purple xes). The corners of the triangle within the plot indicate a rod-like shape (top left), disk-like shape (bottom middle), and sphere-like shape (top right). Source data is provided in the repository and in the Supplementary Information. b NP-likeness score of the PNP collection (244 compounds, blue), compounds from the DrugBank (7472 compounds, orange), and NPs from ChEMBL (30655 compounds, green). c Quantitative estimation of drug-likeness (QED) of the PNP collection (244 compounds, blue), compounds from the DrugBank (7472 compounds, orange), and NPs from ChEMBL (30655 compounds, green). d, e Principal component analysis (PCA) plots (d PC1 and PC2; e PC1 and PC3) of 17 molecular descriptors (number of heavy atoms, molecular weight, number of rings, number of aromatic rings, number of aliphatic rings, number of hydrogen bond donors, number of hydrogen bond acceptors, SLogP, total polar surface area, number of rotatable bonds, number of oxygen atoms, number of nitrogen atoms, number of halogen atoms, number of bridgehead atoms, fraction sp³, number of violations of Lipinski’s rules, number of violations of Veber’s rules) of NPs from ChEMBL (30655 compounds, green), compounds from the DrugBank (7472 compounds, blue), compounds from the Enamine database (49968 compounds, yellow), and compounds from the PNP collection (244 compounds, red) (Expl. Var.: PC1 (37.0%), PC2 (15.7%), PC3 (11.9%)). A plot of PC2 and PC3 can be found at Supplementary Fig. 10. PC = principal component. Source data are provided in the online repository.