5WS3

Crystal structures of human orexin 2 receptor bound to the selective antagonist EMPA determined by serial femtosecond crystallography at SACLA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

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.


Macromolecules
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
PHAROS:  O43614
GTEx:  ENSG00000137252 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9V2J8O43614
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.51α = 90
b = 75.98β = 112.3
c = 96.1γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cheetahdata extraction
CrystFELdata processing
MOLREPphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSTJapan--
MEXTJapan--
JSPSJapan26102725
JSPSJapan15H04338

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Data collection
  • Version 1.2: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references
  • Version 1.4: 2023-11-08
    Changes: Refinement description
  • Version 1.5: 2024-10-23
    Changes: Structure summary