6JIO

Human LXR-beta in complex with a ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.264 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Identify liver X receptor beta modulator building blocks by developing a fluorescence polarization-based competition assay.

Zhang, Z.Chen, H.Chen, Z.Ding, P.Ju, Y.Gu, Q.Xu, J.Zhou, H.

(2019) Eur J Med Chem 178: 458-467

  • DOI: 10.1016/j.ejmech.2019.06.011
  • Primary Citation of Related Structures:  
    6JIO

  • PubMed Abstract: 
  • The liver X receptors (LXRs) of the nuclear receptor family are promising therapeutic targets of multiple diseases like lipid disorders, chronic inflammation, as well as different human cancers. To date, no LXR agonists or antagonists can be used in clinics, emphasizing the importance for discovering new LXR modulators ...

    The liver X receptors (LXRs) of the nuclear receptor family are promising therapeutic targets of multiple diseases like lipid disorders, chronic inflammation, as well as different human cancers. To date, no LXR agonists or antagonists can be used in clinics, emphasizing the importance for discovering new LXR modulators. Fragment-based lead discovery (FBLD) is powerful for designing new scaffolds and new mechanistic drugs, but fragment screening has not been applied to LXRs yet, which might be due to the lack of a specific fragment screening method against the dynamic and hydrophobic ligand binding domain (LBD) of LXRs. Herein, a series of fluorescent tracers were designed, synthesized and tested. The tracer based on hyodeoxycholic acid exhibited a good capability for competitively detecting the ligand binding of LXRβ using a fluorescence polarization approach. Then, 1074 fragments were screened against the LBD of LXRβ (LXRβ-LBD), resulting in 27 binding hits. These fragment hits were further tested using the co-activator recruitment assay and reporter gene assay, and efforts in X-ray crystallography fortunately solved a co-crystal structure of LXRβ-LBD with the fragment F3 (tert-butyl-7-amino-3,4-dihydroisoquinoline-2(1H)-carboxylate). The fluorescence-based fragment screening tool and the newly identified LXRβ binding fragments provide the basis for developing novel LXRβ modulators.


    Organizational Affiliation

    Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China. Electronic address: zhuihao@mail.sysu.edu.cn.



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
BQ3
Query on BQ3

Download Ideal Coordinates CCD File 
A, D
tert-butyl 7-amino-3,4-dihydroisoquinoline-2(1H)-carboxylate
C14 H20 N2 O2
AGRBXKCSGCUXST-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.264 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.137α = 90
b = 106.888β = 90
c = 150.803γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-02-22 
  • Released Date: 2019-10-16 
  • 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: 2019-10-16
    Type: Initial release