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Fig. 1 | Journal of Cheminformatics

Fig. 1

From: Similar compounds versus similar conformers: complementarity between PubChem 2-D and 3-D neighboring sets

Fig. 1

An inherent bias towards 2-D neighboring. CID 63014, a mixture of Tramadol (CID 63015) and HCl, has a drug annotation, but does not have a computed 3-D conformer description in PubChem. As such, CID 63014 cannot have any 3-D neighbors. On the contrary, its parent compound (CID 63015) has a computed 3-D conformer description, and therefore is able to have 3-D neighbors, but does not have a drug annotation. Use of CID 63015 (parent compound) in place of CID 63014 (salt mixture) allows 2-D salt forms to collapse into a single parent and 3-D neighboring methodologies to be compared (conceptually) for the same structure

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