Structural basis for receptor selectivity and inverse agonism in S1P5 receptors

Elizaveta Lyapina, Egor Marin, Anastasiia Gusach, Philipp Orekhov, Andrey Gerasimov, Aleksandra Luginina, Daniil Vakhrameev, Margarita Ergasheva, Margarita Kovaleva, Georgii Khusainov, Polina Khorn, Mikhail Shevtsov, Kirill Kovalev, Sergey Bukhdruker, Ivan Okhrimenko, Petr Popov, Hao Hu, Uwe Weierstall, Wei Liu, Yunje ChoIvan Gushchin, Andrey Rogachev, Gleb Bourenkov, Sehan Park, Gisu Park, Hyo Jung Hyun, Jaehyun Park, Valentin Gordeliy, Valentin Borshchevskiy, Alexey Mishin, Vadim Cherezov

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


The bioactive lysophospholipid sphingosine-1-phosphate (S1P) acts via five different subtypes of S1P receptors (S1PRs) - S1P1-5. S1P5 is predominantly expressed in nervous and immune systems, regulating the egress of natural killer cells from lymph nodes and playing a role in immune and neurodegenerative disorders, as well as carcinogenesis. Several S1PR therapeutic drugs have been developed to treat these diseases; however, they lack receptor subtype selectivity, which leads to side effects. In this article, we describe a 2.2 Å resolution room temperature crystal structure of the human S1P5 receptor in complex with a selective inverse agonist determined by serial femtosecond crystallography (SFX) at the Pohang Accelerator Laboratory X-Ray Free Electron Laser (PAL-XFEL) and analyze its structure-activity relationship data. The structure demonstrates a unique ligand-binding mode, involving an allosteric sub-pocket, which clarifies the receptor subtype selectivity and provides a template for structure-based drug design. Together with previously published S1PR structures in complex with antagonists and agonists, our structure with S1P5-inverse agonist sheds light on the activation mechanism and reveals structural determinants of the inverse agonism in the S1PR family.

Original languageEnglish (US)
Article number4736
JournalNature communications
Issue number1
StatePublished - Dec 2022
Externally publishedYes

ASJC Scopus subject areas

  • General Chemistry
  • General Biochemistry, Genetics and Molecular Biology
  • General Physics and Astronomy


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  • XFEL crystal structure of the human sphingosine 1 phosphate receptor 5 in complex with ONO-5430608

    Lyapina, E. (Contributor), Marin, E. (Contributor), Gusach, A. (Contributor), Orekhov, P. (Contributor), Gerasimov, A. (Contributor), Luginina, A. (Contributor), Vakhrameev, D. (Contributor), Ergasheva, M. (Contributor), Kovaleva, M. (Contributor), Khusainov, G. (Contributor), Khorn, P. (Contributor), Shevtsov, M. (Contributor), Kovalev, K. (Contributor), Bukhdruker, S. (Contributor), Okhrimenko, I. (Contributor), Popov, P. (Contributor), Hu, H. (Contributor), Weierstall, U. (Contributor), Liu, W. (Contributor), Cho, Y. (Contributor), Gushchin, I. (Contributor), Rogachev, A. (Contributor), Bourenkov, G. (Contributor), Park, S. (Contributor), Park, G. (Contributor), Hyun, H. J. (Contributor), Park, J. (Contributor), Gordeliy, V. (Contributor), Borshchevskiy, V. (Contributor), Mishin, A. (Contributor) & Cherezov, V. (Contributor), Protein Data Bank (PDB), Aug 10 2022


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