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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 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 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Orexin receptor type 2A341Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43614
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / 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
 Ligand Interaction
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

View Full Validation Report



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