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 

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Ligand Structure Quality Assessment 


This is version 1.1 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: 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 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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alphaA, C242Homo sapiensMutation(s): 0 
Gene Names: RXRA, NR2B1
UniProt & NIH Common Fund Data Resources
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
PHAROS:  P19793
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19793
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Oxysterols receptor LXR-alphaB, D266Mus musculusMutation(s): 0 
Gene Names: Nr1h3, Lxra
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LO2
Query on LO2
Download Ideal Coordinates CCD File 
F [auth B],
H [auth D]		2-{4-[butyl(3-chloro-4,5-dimethoxybenzyl)amino]phenyl}-1,1,1,3,3,3-hexafluoropropan-2-ol
C22 H24 Cl F6 N O3
QKFWYOZIIUVZRC-UHFFFAOYSA-N		 Ligand Interaction
REA
Query on REA
Download Ideal Coordinates CCD File 
E [auth A],
G [auth C]		RETINOIC ACID
C20 H28 O2
SHGAZHPCJJPHSC-YCNIQYBTSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
REA BindingDB:  3FAL IC50: min: 5.00e+4, max: 5.00e+4 (nM) from 3 assay(s)
LO2 BindingDB:  3FAL IC50: 165 (nM) from 1 assay(s)
Binding MOAD:  3FAL IC50: 165 (nM) from 1 assay(s)
PDBBind:  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

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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