Chemokines and their G-protein-coupled receptors play a diverse role in immune defence by controlling the migration, activation and survival of immune cells1. They are also involved in viral entry, tumour growth and metastasis and hence are important drug targets in a wide range of diseases2,3. Despite very significant efforts by the pharmaceutical industry to develop drugs, with over 50 small-molecule drugs directed at the family entering clinical development, only two compounds have reached the market: maraviroc (CCR5) for HIV infection and plerixafor (CXCR4) for stem-cell mobilization4. The high failure rate may in part be due to limited understanding of the mechanism of action of chemokine antagonists and an inability to optimize compounds in the absence of structural information5. CC chemokine receptor type 9 (CCR9) activation by CCL25 plays a key role in leukocyte recruitment to the gut and represents a therapeutic target in inflammatory bowel disease6. The selective CCR9 antagonist vercirnon progressed to phase 3 clinical trials in Crohn’s disease but efficacy was limited, with the need for very high doses to block receptor activation6. Here we report the crystal structure of the CCR9 receptor in complex with vercirnon at 2.8 Å resolution. Remarkably, vercirnon binds to the intracellular side of the receptor, exerting allosteric antagonism and preventing G-protein coupling. This binding site explains the need for relatively lipophilic ligands and describes another example of an allosteric site on G-protein-coupled receptors7 that can be targeted for drug design, not only at CCR9, but potentially extending to other chemokine receptors.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.



  1. 1.

    Targeting chemokine receptors in allergic disease. Biochem. J. 434, 11–24 (2011)

  2. 2.

    & CCR5 antagonism in HIV infection: current concepts and future opportunities. Annu. Rev. Med. 63, 81–93 (2012)

  3. 3.

    , , , & Chemokine receptor-specific antibodies in cancer immunotherapy: achievements and challenges. Front. Immunol. 6, 12 (2015)

  4. 4.

    , & “Chemokine receptors as therapeutic targets: why aren’t there more drugs?”. Eur. J. Pharmacol. 746, 363–367 (2015)

  5. 5.

    & Chemokine receptor antagonists. J. Med. Chem. 55, 9363–9392 (2012)

  6. 6.

    & CCR9 antagonism: potential in the treatment of inflammatory bowel disease. Clin. Exp. Gastroenterol. 8, 119–130 (2015)

  7. 7.

    & Allosteric modulation as a unifying mechanism for receptor function and regulation. Cell 166, 1084–1102 (2016)

  8. 8.

    , , & Conformational thermostabilization of the β1-adrenergic receptor in a detergent-resistant form. Proc. Natl Acad. Sci. USA 105, 877–882 (2008)

  9. 9.

    et al. The properties of thermostabilised G protein-coupled receptors (StaRs) and their use in drug discovery. Neuropharmacology 60, 36–44 (2011)

  10. 10.

    et al. Characterization of CCX282-B, an orally bioavailable antagonist of the CCR9 chemokine receptor, for treatment of inflammatory bowel disease. J. Pharmacol. Exp. Ther. 335, 61–69 (2010)

  11. 11.

    et al. Structure of the CCR5 chemokine receptor-HIV entry inhibitor maraviroc complex. Science 341, 1387–1390 (2013)

  12. 12.

    et al. Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science 330, 1066–1071 (2010)

  13. 13.

    et al. Structure of class B GPCR corticotropin-releasing factor receptor 1. Nature 499, 438–443 (2013)

  14. 14.

    et al. Extra-helical binding site of a glucagon receptor antagonist. Nature 533, 274–277 (2016)

  15. 15.

    et al. Discovery of a CXCR4 agonist pepducin that mobilizes bone marrow hematopoietic cells. Proc. Natl Acad. Sci. USA 107, 22255–22259 (2010)

  16. 16.

    , & An intracellular allosteric site for a specific class of antagonists of the CC chemokine G protein-coupled receptors CCR4 and CCR5. Mol. Pharmacol. 73, 855–867 (2008)

  17. 17.

    et al. Pharmacological characterization of Sch527123, a potent allosteric CXCR1/CXCR2 antagonist. J. Pharmacol. Exp. Ther. 322, 477–485 (2007)

  18. 18.

    et al. A common intracellular allosteric binding site for antagonists of the CXCR2 receptor. Br. J. Pharmacol. 159, 1429–1439 (2010)

  19. 19.

    et al. SB-656933, a novel CXCR2 selective antagonist, inhibits ex vivo neutrophil activation and ozone-induced airway inflammation in humans. Br. J. Clin. Pharmacol. 72, 282–293 (2011)

  20. 20.

    et al. Identification of a putative intracellular allosteric antagonist binding-site in the CXC chemokine receptors 1 and 2. Mol. Pharmacol. 74, 1193–1202 (2008)

  21. 21.

    et al. Nonpeptidergic allosteric antagonists differentially bind to the CXCR2 chemokine receptor. J. Pharmacol. Exp. Ther. 329, 783–790 (2009)

  22. 22.

    Dancing to the tune of chemokines. Nature Immunol. 2, 129–134 (2001)

  23. 23.

    & Structural insights into agonist-induced activation of G-protein-coupled receptors. Curr. Opin. Struct. Biol. 21, 541–551 (2011)

  24. 24.

    , , , & Unifying family A GPCR theories of activation. Pharmacol. Ther. 143, 51–60 (2014)

  25. 25.

    et al. Crystal structure of the β2 adrenergic receptor-Gs protein complex. Nature 477, 549–555 (2011)

  26. 26.

    et al. Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser. Nature 523, 561–567 (2015)

  27. 27.

    et al. Aryl sulphonamides. US patent 2006/0111351A1 (2006)

  28. 28.

    & Membrane protein orientation and refinement using a knowledge-based statistical potential. BMC Bioinformatics 14, 276–285 (2013)

  29. 29.

    et al. The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis. Nucleic Acids Res. 44 (Suppl. W1), W410–W415 (2016)

  30. 30.

    & Fluorescence-detection size-exclusion chromatography for precrystallization screening of integral membrane proteins. Structure 14, 673–681 (2006)

  31. 31.

    & Crystallizing membrane proteins using lipidic mesophases. Nature Protocols 4, 706–731 (2009)

  32. 32.

    Integration, scaling, space-group assignment and post-refinement. Acta Crystallogr. D 66, 133–144 (2010)

  33. 33.

    Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)

  34. 34.

    & How good are my data and what is the resolution? Acta Crystallogr. D 69, 1204–1214 (2013)

  35. 35.

    et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007)

  36. 36.

    , , & Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010)

  37. 37.

    et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010)

  38. 38.

    et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D 67, 355–367 (2011)

  39. 39.

    et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D 68, 352–367 (2012)

  40. 40.

    , & Constant pressure molecular dynamics algorithms. J. Chem. Phys. 101, 4177–4189 (1994)

  41. 41.

    & Better models by discarding data? Acta Crystallogr. D 69, 1215–1222 (2013)

Download references


We thank D. Axford, R. Owen and D. Sherrell at I24, Diamond Light Source, Oxford, UK, for technical support. We thank colleagues at Heptares Therapeutics for suggestions and comments, and G. Brown and S. Bucknell for assistance in radioligand preparation.

Author information

Author notes

    • Christine Oswald
    • , Mathieu Rappas
    •  & James Kean

    These authors contributed equally to this work.


  1. Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK

    • Christine Oswald
    • , Mathieu Rappas
    • , James Kean
    • , Andrew S. Doré
    • , James C. Errey
    • , Kirstie Bennett
    • , Francesca Deflorian
    • , John A. Christopher
    • , Ali Jazayeri
    • , Jonathan S. Mason
    • , Miles Congreve
    • , Robert M. Cooke
    •  & Fiona H. Marshall


  1. Search for Christine Oswald in:

  2. Search for Mathieu Rappas in:

  3. Search for James Kean in:

  4. Search for Andrew S. Doré in:

  5. Search for James C. Errey in:

  6. Search for Kirstie Bennett in:

  7. Search for Francesca Deflorian in:

  8. Search for John A. Christopher in:

  9. Search for Ali Jazayeri in:

  10. Search for Jonathan S. Mason in:

  11. Search for Miles Congreve in:

  12. Search for Robert M. Cooke in:

  13. Search for Fiona H. Marshall in:


J.K. and A.J. devised and performed the conformational thermostabilization and mutagenesis of the receptor, characterized expression constructs and performed radioligand binding analysis of mutants. Computational analysis of the structure and modelling was performed by F.D. and J.S.M. A.S.D. established the platform/protocols for LCP crystallization and solved the structure. J.C.E. supported expression and scouted purification of the final StaR. M.R. designed and characterized all constructs, collected and processed X-ray diffraction data and solved the structure. C.O. optimized purification, performed LCP crystallization, harvested crystals, collected and processed X-ray diffraction data, and solved and refined the structure. K.B. performed and analysed the pharmacology data. J.A.C. and M.C. identified and sourced the chemical compound(s) used in the study. Project management was performed by J.A.C., R.M.C. and F.H.M. The manuscript was prepared by A.S.D., C.O., F.D., M.C. and F.H.M. All authors contributed to the final editing and approval of the manuscript.

Competing interests

The authors are employees of Heptares Therapeutics and are shareholders of Sosei Group, the parent company of Heptares. Heptares is a drug discovery and development company working in the field of G-protein-coupled receptor structure-based drug design.

Corresponding author

Correspondence to Fiona H. Marshall.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Figure

    This file contains Supplementary Figure 1, preparation of [3H]vercirnon and vercirnon.

About this article

Publication history






Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.