3FAL

humanRXR alpha & mouse LXR alpha complexed with Retenoic acid and GSK2186


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure-guided design of N-phenyl tertiary amines as transrepression-selective liver X receptor modulators with anti-inflammatory activity.

Chao, E.Y.Caravella, J.A.Watson, M.A.Campobasso, N.Ghisletti, S.Billin, A.N.Galardi, C.Wang, P.Laffitte, B.A.Iannone, M.A.Goodwin, B.J.Nichols, J.A.Parks, D.J.Stewart, E.Wiethe, R.W.Williams, S.P.Smallwood, A.Pearce, K.H.Glass, C.K.Willson, T.M.Zuercher, W.J.Collins, J.L.

(2008) J Med Chem 51: 5758-5765

  • DOI: https://doi.org/10.1021/jm800612u
  • Primary Citation of Related Structures:  
    3FAL

  • PubMed Abstract: 

    A cocrystal structure of T1317 (3) bound to hLXRbeta was utilized in the design of a series of substituted N-phenyl tertiary amines. Profiling in binding and functional assays led to the identification of LXR modulator GSK9772 ( 20) as a high-affinity LXRbeta ligand (IC 50 = 30 nM) that shows separation of anti-inflammatory and lipogenic activities in human macrophage and liver cell lines, respectively. A cocrystal structure of the structurally related analog 19 bound to LXRbeta reveals regions within the receptor that can affect receptor modulation through ligand modification. Mechanistic studies demonstrate that 20 is greater than 10-fold selective for LXR-mediated transrepression of proinflammatory gene expression versus transactivation of lipogenic signaling pathways, thus providing an opportunity for the identification of LXR modulators with improved therapeutic indexes.


  • Organizational Affiliation

    GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina 27709, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alpha
A, C
242Homo sapiensMutation(s): 0 
Gene Names: RXRANR2B1
UniProt & NIH Common Fund Data Resources
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
PHAROS:  P19793
GTEx:  ENSG00000186350 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19793
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Oxysterols receptor LXR-alpha
B, D
266Mus musculusMutation(s): 0 
Gene Names: Nr1h3Lxra
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Z0Y9 (Mus musculus)
Explore Q9Z0Y9 
Go to UniProtKB:  Q9Z0Y9
IMPC:  MGI:1352462
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Z0Y9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
REA BindingDB:  3FAL IC50: min: 5.00e+4, max: 5.00e+4 (nM) from 3 assay(s)
LO2 PDBBind:  3FAL IC50: 165 (nM) from 1 assay(s)
BindingDB:  3FAL IC50: 165 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.212α = 90
b = 90.002β = 111.88
c = 101.311γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Derived calculations