1UPW

Crystal structure of the human Liver X receptor beta ligand binding domain in complex with a synthetic agonist

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.250 

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This is version 1.3 of the entry. See complete history. 


Literature

Crystal Structure of the Human Liver X Receptor Beta Ligand-Binding Domain in Complex with a Synthetic Agonist

Hoerer, S., Schmid, A., Heckel, A., Budzinski, R.M., Nar, H.

(2003) J Mol Biol 334: 853

  • DOI: 10.1016/j.jmb.2003.10.033
  • Primary Citation of Related Structures:  
    1UPW, 1UPV

  • PubMed Abstract: 

    • LXRbeta belongs to the nuclear hormone receptor superfamily of ligand-activated transcription factors. Its natural ligands are supposed to be oxidised derivatives of cholesterol. Stimulation of LXRbeta by agonists activates a number of genes that are involved in the regulation of lipid metabolism and cholesterol efflux from cells ...

    LXRbeta belongs to the nuclear hormone receptor superfamily of ligand-activated transcription factors. Its natural ligands are supposed to be oxidised derivatives of cholesterol. Stimulation of LXRbeta by agonists activates a number of genes that are involved in the regulation of lipid metabolism and cholesterol efflux from cells. Therefore, LXRbeta may represent a novel therapeutic target for the treatment of dyslipidemia and atherosclerosis.Here, we report the X-ray crystal structure of the LXRbeta ligand-binding domain in complex with a synthetic agonist, T-0901317. This compound occupies the ligand-binding pocket of the receptor, forms numerous lipophilic contacts with the protein and one crucial hydrogen bond to His435 and stabilises the agonist conformation of the receptor ligand-binding domain. The recruitment of the AF2-region of the protein is not achieved via direct polar interactions of the ligand with protein side-chains of this helical segment, but rather via few hydrophobic contacts and probably more importantly via indirect effects involving the pre-orientation of side-chains that surround the ligand-binding pocket and form the interface to the AF2-helix. On the basis of these results we propose a binding mode and a mechanism of action for the putative natural ligands, oxidised derivatives of cholesterol.

    Organizational Affiliation: 

    Department of Lead Discovery, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, D-88397 Biberach/Riss, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
OXYSTEROLS RECEPTOR LXR-BETA A257Homo sapiensMutation(s): 0 
Gene Names: NR1H2, LXRB, NER, UNR
Find proteins for P55055 (Homo sapiens)
Explore P55055 
Go to UniProtKB:  P55055
NIH Common Fund Data Resources
PHAROS:  P55055
GTEx:  ENSG00000131408
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
444
Query on 444
Download Ideal Coordinates CCD File 
A
N-(2,2,2-TRIFLUOROETHYL)-N-{4-[2,2,2-TRIFLUORO-1-HYDROXY-1-(TRIFLUOROMETHYL)ETHYL]PHENYL}BENZENESULFONAMIDE
C17 H12 F9 N O3 S
SGIWFELWJPNFDH-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
444EC50:  230   nM  BindingDB
444Kd:  103   nM  BindingDB
444EC50:  15   nM  BindingDB
444EC50:  16   nM  BindingDB
444EC50:  19   nM  BindingDB
444EC50:  300   nM  BindingDB
444EC50:  21   nM  BindingDB
444EC50:  20   nM  BindingDB
444IC50:  9000   nM  BindingDB
444EC50:  400   nM  BindingDB
444EC50:  110   nM  BindingDB
444EC50:  103   nM  BindingDB
444IC50:  26000   nM  BindingDB
444IC50:  100   nM  BindingDB
444EC50:  120   nM  BindingDB
444EC50:  135   nM  BindingDB
444EC50:  140   nM  BindingDB
444EC50:  8   nM  BindingDB
444EC50:  130   nM  BindingDB
444EC50:  156   nM  BindingDB
444EC50:  170   nM  BindingDB
444EC50:  160   nM  BindingDB
444IC50:  70   nM  BindingDB
444EC50:  178   nM  BindingDB
444EC50:  198   nM  BindingDB
444EC50:  53   nM  BindingDB
444Ki:  17   nM  BindingDB
444IC50:  13   nM  BindingDB
444EC50:  4.699999809265137   nM  BindingDB
444EC50:  66   nM  BindingDB
444EC50:  75   nM  BindingDB
444EC50:  85   nM  BindingDB
444IC50:  9   nM  BindingDB
444EC50:  90   nM  BindingDB
444IC50:  10   nM  BindingDB
444EC50:  100   nM  BindingDB
444IC50:  30   nM  BindingDB
444EC50:  410   nM  BindingDB
444EC50:  30   nM  BindingDB
444IC50:  20   nM  BindingDB
444EC50:  50   nM  BindingDB
444EC50:  800   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.250 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.22α = 90
b = 43.276β = 90
c = 51.615γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-28
    Changes: Source and taxonomy