7XRR | pdb_00007xrr

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

• PDB DOI: https://doi.org/10.2210/pdb7XRR/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2022-05-11 Released: 2022-11-23 
• Deposition Author(s): Asada, H., Im, D., Iwata, S.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 
  0.287 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.275 (Depositor), 0.275 (DCC) 
• R-Value Observed: 
  0.276 (Depositor) 

Starting Model: experimental

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

• PubMed: 36417909 
• DOI: https://doi.org/10.1016/j.str.2022.11.001
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan. Electronic address: [e-mail].
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.
Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan; Membrane Protein Research and Molecular Chirality Research Centers, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan.
Department of Medical Chemistry, Kansai Medical University, Hirakata 573-1010, Japan.
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 39.97 kDa 
• Atom Count: 2,553 
• Modeled Residue Count: 309 
• Deposited Residue Count: 341 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orexin receptor type 2	A	341	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NRK (Subject of Investigation/LOI)	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

Binding Affinity Annotations
ID	Source	Binding Affinity
NRK	BindingDB:  7XRR	Ki: min: 0.44, max: 3 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free:  0.287 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.275 (Depositor), 0.275 (DCC) 
• R-Value Observed: 0.276 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.59	α = 90
b = 90.23	β = 90
c = 112.32	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-23 
Deposition Author(s): Asada, H., Im, D., Iwata, S.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101079
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101070
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101083

Revision History  

• 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
• Version 1.4: 2024-11-06
  Changes: Structure summary