Crystal structure of human orexin 2 receptor bound to the selective antagonist EMPA determined by the synchrotron light source at SPring-8.

Experimental Data Snapshot

  • Resolution: 1.96 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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This is version 1.2 of the entry. See complete history


Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA

Suno, R.Kimura, K.T.Nakane, T.Yamashita, K.Wang, J.Fujiwara, T.Yamanaka, Y.Im, D.Horita, S.Tsujimoto, H.Tawaramoto, M.S.Hirokawa, T.Nango, E.Tono, K.Kameshima, T.Hatsui, T.Joti, Y.Yabashi, M.Shimamoto, K.Yamamoto, M.Rosenbaum, D.M.Iwata, S.Shimamura, T.Kobayashi, T.

(2018) Structure 26: 7-19.e5

  • DOI: https://doi.org/10.1016/j.str.2017.11.005
  • Primary Citation of Related Structures:  
    5WQC, 5WS3

  • PubMed Abstract: 

    Orexin peptides in the brain regulate physiological functions such as the sleep-wake cycle, and are thus drug targets for the treatment of insomnia. Using serial femtosecond crystallography and multi-crystal data collection with a synchrotron light source, we determined structures of human orexin 2 receptor in complex with the subtype-selective antagonist EMPA (N-ethyl-2-[(6-methoxy-pyridin-3-yl)-(toluene-2-sulfonyl)-amino]-N-pyridin-3-ylmethyl-acetamide) at 2.30-Å and 1.96-Å resolution. In comparison with the non-subtype-selective antagonist suvorexant, EMPA contacted fewer residues through hydrogen bonds at the orthosteric site, explaining the faster dissociation rate. Comparisons among these OX 2 R structures in complex with selective antagonists and previously determined OX 1 R/OX 2 R structures bound to non-selective antagonists revealed that the residue at positions 2.61 and 3.33 were critical for the antagonist selectivity in OX 2 R. The importance of these residues for binding selectivity to OX 2 R was also revealed by molecular dynamics simulation. These results should facilitate the development of antagonists for orexin receptors.

  • Organizational Affiliation

    Department of Medical Chemistry and Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Orexin receptor type 2,GlgA glycogen synthase,Orexin receptor type 2560Homo sapiensPyrococcus abyssi GE5Mutation(s): 1 
Gene Names: HCRTR2PAB2292
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9V2J8 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V2J8 
Go to UniProtKB:  Q9V2J8
Find proteins for O43614 (Homo sapiens)
Explore O43614 
Go to UniProtKB:  O43614
GTEx:  ENSG00000137252 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9V2J8O43614
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
7MA BindingDB:  5WQC Ki: min: 1.1, max: 1000 (nM) from 2 assay(s)
IC50: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.96 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.13α = 90
b = 75.52β = 111.39
c = 95.93γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Science and Technology Agency (JST)Japantarget-driven R&D (A-STEP)
Japan Science and Technology Agency (JST)Japanthe Research Acceleration Program
Toray Science FoundationJapan--
Takeda Science FoundationJapan--
the Naito FoundationJapan--
Ministry of Education, Culture, Sports, Science and Technology (MEXT)Japanthe Platform for Drug Discovery, Informatics, and Structural Life Science (PDIS)
the Ministry of Education, Culture, Sports, Science and Technology (MEXT)Japanthe X-ray Free-Electron Laser Priority Strategy Program
the Welch FoundationUnited StatesI-1770

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2017-12-27
    Changes: Database references
  • Version 1.2: 2018-01-17
    Changes: Database references