3IPS

X-ray structure of benzisoxazole synthetic agonist bound to the LXR-alpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-ray structures of the LXRalpha LBD in its homodimeric form and implications for heterodimer signaling.

Fradera, X.Vu, D.Nimz, O.Skene, R.Hosfield, D.Wynands, R.Cooke, A.J.Haunso, A.King, A.Bennett, D.J.McGuire, R.Uitdehaag, J.C.

(2010) J.Mol.Biol. 399: 120-132

  • DOI: 10.1016/j.jmb.2010.04.005
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Liver X receptors (LXRs) are nuclear receptors that are central regulators of cholesterol homeostasis, and synthetic LXR agonists have shown promise as promoters of reverse cholesterol transport and anti-inflammatory agents. Here, we present three X- ...

    Liver X receptors (LXRs) are nuclear receptors that are central regulators of cholesterol homeostasis, and synthetic LXR agonists have shown promise as promoters of reverse cholesterol transport and anti-inflammatory agents. Here, we present three X-ray structures of three different agonists bound to the ligand binding domain of LXRalpha. These compounds are GW3965, F(3)methylAA, and a benzisoxazole urea, and we show that these diverse chemical scaffolds address common structural themes, leading to high binding affinity for LXR. Our structures show the LXRalpha ligand binding domain in its homodimeric form, an arrangement previously thought to be stereochemically difficult. A comparison with existing structures of the LXRbeta homodimer and LXRalpha:RXR (retinoid X receptor) heterodimers explains differences in dimer affinity and leads us to propose a model for allosteric activation in nuclear receptor dimers, in which an unactivated RXR partner provides an inhibitory tail wrap to the cofactor binding pocket of LXR.


    Organizational Affiliation

    Department of Chemistry, Merck Research Labs, Newhouse, ML1 5SH, Scotland, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oxysterols receptor LXR-alpha
A, B
283Homo sapiensMutation(s): 0 
Gene Names: NR1H3 (LXRA)
Find proteins for Q13133 (Homo sapiens)
Go to Gene View: NR1H3
Go to UniProtKB:  Q13133
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 1
C, D
25Homo sapiensMutation(s): 0 
Gene Names: NCOA1 (BHLHE74, SRC1)
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to Gene View: NCOA1
Go to UniProtKB:  Q15788
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
O90
Query on O90

Download SDF File 
Download CCD File 
A, B
{3-chloro-4-[(3-{[7-propyl-3-(trifluoromethyl)-1,2-benzisoxazol-6-yl]oxy}propyl)sulfanyl]phenyl}acetic acid
C22 H21 Cl F3 N O4 S
TZBRFAASYWFUGK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
O90EC50: 35 - 5900 nM (100) BINDINGDB
O90IC50: 32 - 35 nM (100) BINDINGDB
O90Ki: 64 nM BINDINGMOAD
O90Ki: 64 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.255 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 123.051α = 90.00
b = 123.051β = 90.00
c = 91.636γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
CrystalCleardata scaling
REFMACrefinement
MOLREPphasing
CrystalCleardata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance