6K9M

Human LXR-beta in complex with an agonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of novel liver X receptor inverse agonists as lipogenesis inhibitors.

Chen, Z.Chen, H.Zhang, Z.Ding, P.Yan, X.Li, Y.Zhang, S.Gu, Q.Zhou, H.Xu, J.

(2020) Eur J Med Chem 206: 112793-112793

  • DOI: 10.1016/j.ejmech.2020.112793
  • Primary Citation of Related Structures:  
    6K9M

  • PubMed Abstract: 
  • Based on the co-crystal structures of LXRβ and its agonists (spiro [pyrrolidine-3,3'-oxindole] derivatives) discovered by us previously, we designed and synthesized a compound library to explore the agonistic activities. The library was screened with luciferase reporter assays, interestingly, it resulted in the discovery of 10 LXR inverse agonists besides 5 LXR agonists ...

    Based on the co-crystal structures of LXRβ and its agonists (spiro [pyrrolidine-3,3'-oxindole] derivatives) discovered by us previously, we designed and synthesized a compound library to explore the agonistic activities. The library was screened with luciferase reporter assays, interestingly, it resulted in the discovery of 10 LXR inverse agonists besides 5 LXR agonists. To clarify the mechanism of the actions, we conducted molecular dynamics (MD) simulations on the LXR and inverse agonists complexes, and revealed that H3, H11 and H12 configurations are the key to turn on agonism or inverse agonism status for LXR. Binding tightly with H3, pushing H11 out and destabilizing H12 could form a bigger hydrophobic groove to accommodate NCOR1 to turn on LXR inverse agonism. The inverse agonist 10rr was further studied, and found as a lipogenesis inhibitor through down-regulating LXR target genes SREBP-1c, ACC, FAS and SCD-1, and demonstrated lipid-lowering effects in 3T3-L1 cells, HepG2 cells and mice with Triton WR-1339-induced hyperlipidemia. Therefore, we have proved that LXR inverse agonists can be promising agents for hyperlipidemia treatment.


    Organizational Affiliation

    Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China; School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China. Electronic address: junxu@biochemomes.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Oxysterols receptor LXR-beta ABCD274Homo sapiensMutation(s): 4 
Gene Names: NR1H2LXRBNERUNR
Find proteins for P55055 (Homo sapiens)
Explore P55055 
Go to UniProtKB:  P55055
NIH Common Fund Data Resources
PHAROS:  P55055
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D43
Query on D43

Download Ideal Coordinates CCD File 
A, B, C, D
~{tert}-butyl (2'~{S},3~{S})-2-oxidanylidene-2'-propan-2-yl-spiro[1~{H}-indole-3,3'-pyrrolidine]-1'-carboxylate
C19 H26 N2 O3
PENVAQPGQMBKCU-KXBFYZLASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.863α = 90
b = 105.356β = 90
c = 150.43γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-06-16 
  • Released Date: 2020-06-17 
  • Deposition Author(s): Zhang, Z., Zhou, H.

Funding OrganizationLocationGrant Number
National Science Foundation (China)China81773636

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-10-07
    Changes: Database references