5WQC

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 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 s ...

    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; Japan Science and Technology Agency (JST) and Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (CREST), Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan. Electronic address: kobayashi.takuya.4r@kyoto-u.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Orexin receptor type 2,GlgA glycogen synthase,Orexin receptor type 2A560Homo sapiensPyrococcus abyssi GE5Mutation(s): 1 
Gene Names: HCRTR2
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs): Class A
Protein: 
OX2 orexin receptor with bound antagonist EMPA
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
NIH Common Fund Data Resources
PHAROS  O43614
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7MA
Query on 7MA

Download CCD File 
A
N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl)sulfonyl-amino]-N-(pyridin-3-ylmethyl)ethanamide
C23 H26 N4 O4 S
KJPHTXTWFHVJIG-UHFFFAOYSA-N
 Ligand Interaction
OLA
Query on OLA

Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
1PE
Query on 1PE

Download CCD File 
A
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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
JSPSJapan26102725
JSPSJapan15H04338
JSPSJapan15K08268
JSPSJapan15H06862
the Welch FoundationUnited StatesI-1770

Revision History 

  • 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