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. 2022 Sep 6;12:15100. doi: 10.1038/s41598-022-19363-6

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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ED-based 3D molecule generation for HPK1. (a) Binding pocket and reference ligand (PDB code 7KAC). Experimental ED (2Fo-Fc map at 1.2 σ contour level) for the pocket and ligand is shown as blue mesh. (b) Pocket ED with ligand removed. (c) Generated filler ED. For the rainbow color scheme, red indicates a strong ED intensity, and blue indicates a weak ED intensity. The extension of generated ED to the region originally occupied by water molecules and cavities originally unoccupied is indicated by red arrows. (d) Reconstructed ED generated based on filler ED. (e) Hinge binding fragments fitted in the reconstructed ED; map skeletons shown as white lines. (f) Examples of generated molecules and their map skeletons aligned with reconstructed ED. (g) List of examples of generated molecules.