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 

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Ligand Structure Quality Assessment 


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 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 ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Orexin receptor type 2,GlgA glycogen synthase,Orexin receptor type 2A560Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9V2J8O43614
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7MA
Query on 7MA

Download Ideal Coordinates CCD File 
B [auth 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 Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
H [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
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

  • 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

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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
JSPSJapan26102725
JSPSJapan15H04338
JSPSJapan15K08268
JSPSJapan15H06862
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