7XRR

Crystal structure of the human OX2R bound to the insomnia drug lemborexant.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.276 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Molecular basis for anti-insomnia drug design from structure of lemborexant-bound orexin 2 receptor.

Asada, H.Im, D.Hotta, Y.Yasuda, S.Murata, T.Suno, R.Iwata, S.

(2022) Structure 30: 1582-1589.e4

  • DOI: https://doi.org/10.1016/j.str.2022.11.001
  • Primary Citation of Related Structures:  
    7XRR

  • PubMed Abstract: 

    Orexin receptors are a family of G protein-coupled receptors that consist of two subtypes: orexin-1 receptors (OX1Rs) and OX2Rs. They are expressed throughout the central nervous system and are involved in regulating the sleep-wake cycle. The development of antagonists to orexin receptors has become important in drug discovery because modulation of these receptors can lead to novel treatments for diseases related to the regulation of sleep and wakefulness, such as insomnia. In this study, we determined that the structure of OX2R bound to lemborexant, a dual orexin receptor antagonist (DORA), at 2.89 Å resolution. Comparisons of kinetic and dynamic properties of DORAs based on structures and simulations suggest that the enthalpy of molecular binding to receptors and the entropy derived from intramolecular structure can be separately controlled. These results complement existing structural information and allow us to discuss the usefulness of pharmacophore models and target selectivity to OXRs.


  • Organizational Affiliation

    Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan. Electronic address: asada.hidetsugu.4s@kyoto-u.ac.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Orexin receptor type 2341Homo sapiensMutation(s): 4 
Gene Names: HCRTR2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
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 GroupO43614
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NRK (Subject of Investigation/LOI)
Query on NRK

Download Ideal Coordinates CCD File 
B [auth A](1~{R},2~{S})-2-[(2,4-dimethylpyrimidin-5-yl)oxymethyl]-~{N}-(5-fluoranylpyridin-2-yl)-2-(3-fluorophenyl)cyclopropane-1-carboxamide
C22 H20 F2 N4 O2
MUGXRYIUWFITCP-PGRDOPGGSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.276 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.59α = 90
b = 90.23β = 90
c = 112.32γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP21am0101079
Japan Agency for Medical Research and Development (AMED)JapanJP21am0101070
Japan Agency for Medical Research and Development (AMED)JapanJP21am0101083

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2022-12-14
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description