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AlphaFold3 versus experimental structures: assessment of the accuracy in ligand-bound G protein-coupled receptors

Acta Pharmacologica Sinica volume 46, pages 1111–1122 (2025)Cite this article

Abstract

G protein-coupled receptors (GPCRs) are critical drug targets involved in numerous physiological processes, yet many of their structures remain unresolved due to inherent flexibility and diverse ligand interactions. This study systematically evaluates the accuracy of AlphaFold3-predicted GPCR structures compared to experimentally determined structures, with a primary focus on ligand-bound states. Our analysis reveals that while AlphaFold3 shows improved performance over AlphaFold2 in predicting overall GPCR backbone architecture, significant discrepancies persist in ligand-binding poses, particularly for ions, peptides, and proteins. Despite advancements, these limitations constrain the utility of AlphaFold3 models in functional studies and structure-based drug design, where high-resolution details of ligand interactions are crucial. We assess the accuracy of predicted structures across various ligand types, quantifying deviations in binding pocket geometries and ligand orientations. Our findings highlight specific challenges in the computational prediction of ligand-bound GPCR structures, emphasizing areas where further refinement is needed. This study provides valuable insights for researchers using AlphaFold3 in GPCR studies, underscores the ongoing necessity for experimental structure determination, and offers direction for improving protein–ligand interaction predictions in future computational models.

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Fig. 1: Global comparison of AF3-predicted models and experimental GPCR structures.
Fig. 2: Comparative analysis of AF3 predictions and experimental structures for GPCR-peptide complexes.
Fig. 3: Comparative analysis of AF3 predictions and experimental structures for GPCR-ion or protein complexes.
Fig. 4: Comparative analysis of AF3 predictions and experimental structures for GPCR-antibody complexes.
Fig. 5: Comparative analysis of AF3 predictions and experimental structures for GPCR-G protein complexes.
Fig. 6: Flexible domain prediction by AF3.
Fig. 7: Multidisciplinary approaches to enhance AF3 predictions.

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Acknowledgements

The project was supported by the National Key R&D Program of China (2022YFC2703105 to HEX); The National Natural Science Foundation of China (32130022, 82121005); CAS Strategic Priority Research Program (XDB37030103 to HEX); Shanghai Municipal Science and Technology Major Project (2019SHZDZX02 to HEX); Shanghai Municipal Science and Technology Major Project (HEX); the Lingang Laboratory, Grant No. LG-GG-202204-01 (HEX). The authors acknowledge the Beijing Super Cloud Center (BSCC) for providing HPC resources that have contributed to the research results reported within this paper. URL: http://www.blsc.cn/.

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  1. These authors contributed equally: Xin-heng He, Jun-rui Li, Shi-yi Shen

Authors and Affiliations

  1. State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China

    Xin-heng He, Jun-rui Li, Shi-yi Shen & H. Eric Xu

  2. University of Chinese Academy of Sciences, Beijing, 100049, China

    Xin-heng He, Shi-yi Shen & H. Eric Xu

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  1. Xin-heng He
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Correspondence to H. Eric Xu.

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He, Xh., Li, Jr., Shen, Sy. et al. AlphaFold3 versus experimental structures: assessment of the accuracy in ligand-bound G protein-coupled receptors. Acta Pharmacol Sin 46, 1111–1122 (2025). https://doi.org/10.1038/s41401-024-01429-y

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