6S4T

LXRbeta ligand binding domain in comlpex with small molecule inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.205 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural analysis identifies an escape route from the adverse lipogenic effects of liver X receptor ligands.

Belorusova, A.Y.Evertsson, E.Hovdal, D.Sandmark, J.Bratt, E.Maxvall, I.Schulman, I.G.Akerblad, P.Lindstedt, E.L.

(2019) Commun Biol 2: 431-431

  • DOI: https://doi.org/10.1038/s42003-019-0675-0
  • Primary Citation of Related Structures:  
    6S4N, 6S4T, 6S4U, 6S5K

  • PubMed Abstract: 

    Liver X receptors (LXRs) are attractive drug targets for cardiovascular disease treatment due to their role in regulating cholesterol homeostasis and immunity. The anti-atherogenic properties of LXRs have prompted development of synthetic ligands, but these cause major adverse effects-such as increased lipogenesis-which are challenging to dissect from their beneficial activities. Here we show that LXR compounds displaying diverse functional responses in animal models induce distinct receptor conformations. Combination of hydrogen/deuterium exchange mass spectrometry and multivariate analysis allowed identification of LXR regions differentially correlating with anti-atherogenic and lipogenic activities of ligands. We show that lipogenic compounds stabilize active states of LXRα and LXRβ while the anti-atherogenic expression of the cholesterol transporter ABCA1 is associated with the ligand-induced stabilization of LXRα helix 3. Our data indicates that avoiding ligand interaction with the activation helix 12 while engaging helix 3 may provide directions for development of ligands with improved therapeutic profiles.


  • Organizational Affiliation

    1Medicinal Chemistry, Respiratory, Inflammation and Autoimmunity, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oxysterols receptor LXR-beta245Homo sapiensMutation(s): 0 
Gene Names: NR1H2LXRBNERUNR
UniProt & NIH Common Fund Data Resources
Find proteins for P55055 (Homo sapiens)
Explore P55055 
Go to UniProtKB:  P55055
PHAROS:  P55055
GTEx:  ENSG00000131408 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55055
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KVB (Subject of Investigation/LOI)
Query on KVB

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
2-[4-[[3-[3-(phenylmethyl)-8-(trifluoromethyl)quinolin-4-yl]phenoxy]methyl]phenyl]ethanoic acid
C32 H24 F3 N O3
VXHRQVMQVYQGQG-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
KVB BindingDB:  6S4T IC50: min: 2, max: 2000 (nM) from 3 assay(s)
EC50: min: 71, max: 93 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.205 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.275α = 90
b = 135.275β = 90
c = 69.734γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references