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Structure of the human histamine H1 receptor complex with doxepin

Nature volume 475, pages 6570 (07 July 2011) | Download Citation


The biogenic amine histamine is an important pharmacological mediator involved in pathophysiological processes such as allergies and inflammations. Histamine H1 receptor (H1R) antagonists are very effective drugs alleviating the symptoms of allergic reactions. Here we show the crystal structure of the H1R complex with doxepin, a first-generation H1R antagonist. Doxepin sits deep in the ligand-binding pocket and directly interacts with Trp 4286.48, a highly conserved key residue in G-protein-coupled-receptor activation. This well-conserved pocket with mostly hydrophobic nature contributes to the low selectivity of the first-generation compounds. The pocket is associated with an anion-binding region occupied by a phosphate ion. Docking of various second-generation H1R antagonists reveals that the unique carboxyl group present in this class of compounds interacts with Lys 1915.39 and/or Lys 179ECL2, both of which form part of the anion-binding region. This region is not conserved in other aminergic receptors, demonstrating how minor differences in receptors lead to pronounced selectivity differences with small molecules. Our study sheds light on the molecular basis of H1R antagonist specificity against H1R.

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Protein Data Bank

Data deposits

The coordinates and the structure factors have been deposited in the Protein Data Bank under the accession code 3RZE.


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This work was supported by the ERATO Human Receptor Crystallography Project from the Japan Science and Technology Agency and by the Targeted Proteins Research Program of MEXT (S.I.), Japan; the NIH Common Fund grant P50 GM073197 for technology development (R.C.S.) and NIH PSI:Biology grant U54 GM094618 (R.C.S., V.C., V.K. and R.A.); R.A. was also partly funded by NIH R01 GM071872. The work was also partly funded by the Biotechnology and Biological Sciences Research Council (BBSRC) BB/G023425/1 (S.I.), Grant-in-Aid for challenging Exploratory Research (T.S.), the Mochida Memorial Foundation for Medical and Pharmaceutical Research (T.S. and T.K.), Takeda Scientific Foundation (M.S.) and the Sumitomo Foundation (T.K.). A part of the work was performed in the Membrane Protein Laboratory funded by the Wellcome Trust (grant 062164/ Z/00/Z) at the Diamond Light Source Limited and at The Scripps Research Institute. We thank D. Axford, R. Owen and G. Evans for help with data collection at I24 of the Diamond Light Source Limited, H. Wu for help with the preparation of Supplementary Fig. 1 and Q. Xu for help on validation of data processing and A. Walker for assistance with manuscript preparation. The authors acknowledge Y. Zheng (The Ohio State University) and M. Caffrey, Trinity College (Dublin, Ireland), for the loan of the in meso robot (built with support from the NIH (GM075915), the National Science Foundation (IIS0308078), and Science Foundation Ireland (02-IN1-B266)). S.I. is thankful for the help of L. E. Johnson, a co-founder of the Diamond-MPL Project and R. Tanaka, the technical coordinator of the ERATO Human Receptor Crystallography Project.

Author information

Author notes

    • Tatsuro Shimamura
    •  & Mitsunori Shiroishi

    These authors contributed equally to this work.


  1. Human Receptor Crystallography Project, ERATO, Japan Science and Technology Agency, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan

    • Tatsuro Shimamura
    • , Mitsunori Shiroishi
    • , Simone Weyand
    • , Hirokazu Tsujimoto
    • , Takuya Kobayashi
    •  & So Iwata
  2. Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-Ku, Kyoto 606-8501, Japan

    • Tatsuro Shimamura
    • , Mitsunori Shiroishi
    • , Hirokazu Tsujimoto
    • , Takuya Kobayashi
    •  & So Iwata
  3. Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA

    • Tatsuro Shimamura
    • , Vadim Cherezov
    • , Wei Liu
    • , Gye Won Han
    •  & Raymond C. Stevens
  4. Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan

    • Mitsunori Shiroishi
  5. Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK

    • Simone Weyand
    •  & So Iwata
  6. Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE, UK

    • Simone Weyand
    • , Graeme Winter
    •  & So Iwata
  7. Skaggs School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, USA

    • Vsevolod Katritch
    •  & Ruben Abagyan
  8. Systems and Structural Biology Center, RIKEN, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama 230-0045 Japan

    • So Iwata


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T.S. purified and crystallized the receptor in LCP, optimized crystallization conditions, grew crystals for data collection, solved and refined the structure, and prepared the manuscript. M.S. designed, characterized and screened the constructs, purified the receptor, and prepared the manuscript. S.W. and S.I. collected the data and processed diffraction data with G.W.H. H.T. expressed the receptor, prepared the membrane, and performed the ligand-binding assay. V.K. and R.A. performed flexible ligand-receptor docking, and prepared the manuscript. V.C. assisted with the crystallization in LCP and prepared the manuscript. W.L. performed the thermal stability assay and assisted with the crystallization in LCP. G.W.H. refined the structure and assisted with preparing the manuscript. T.K. designed the receptor production strategy and assisted with preparing the manuscript. R.C.S. and S.I. were responsible for the overall project strategy and management and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Takuya Kobayashi or Raymond C. Stevens or So Iwata.

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