6K9H

Human LXR-beta in complex with an agonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.261 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Discovery of new LXR beta agonists as glioblastoma inhibitors.

Chen, H.Chen, Z.Zhang, Z.Li, Y.Zhang, S.Jiang, F.Wei, J.Ding, P.Zhou, H.Gu, Q.Xu, J.

(2020) Eur J Med Chem 194: 112240-112240

  • DOI: 10.1016/j.ejmech.2020.112240
  • Primary Citation of Related Structures:  
    6K9G, 6K9H

  • PubMed Abstract: 
  • Discovery and optimization of selective liver X receptor β (LXRβ) agonists are challenging due to the high homology of LXRα and LXRβ in the ligand-binding domain. There is only one different residue (Val versus Ile) at the ligand-binding pocket of LXRs. With machine learning methods, we identified pan LXR agonists with a novel scaffold (spiro[pyrrolidine-3,3'-oxindole]) ...

    Discovery and optimization of selective liver X receptor β (LXRβ) agonists are challenging due to the high homology of LXRα and LXRβ in the ligand-binding domain. There is only one different residue (Val versus Ile) at the ligand-binding pocket of LXRs. With machine learning methods, we identified pan LXR agonists with a novel scaffold (spiro[pyrrolidine-3,3'-oxindole]). Then, we figured out the mechanism of LXR isoform selectivity from co-crystal structures. Based on the mechanism and the new scaffold, LXRβ selective agonists were designed and synthesized. This led to the discovery of LXRβ agonists 4-7rr, 4-13 and 4-13rr with IC 50 values ranging from 1.78 to 6.36 μM against glioblastoma in vitro. Treatment with 50 mg/kg/day of 4-13 for 15 days significantly reduced tumor growth using an in vivo xenograft glioblastoma model.


    Organizational Affiliation

    Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Research Center for Drug Discovery at School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China. Electronic address: junxu@biochemomes.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Oxysterols receptor LXR-beta AB274Homo 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
D40
Query on D40

Download Ideal Coordinates CCD File 
A, B
~{tert}-butyl (2'~{S},3~{S})-2-oxidanylidene-2'-phenyl-spiro[1~{H}-indole-3,3'-pyrrolidine]-1'-carboxylate
C22 H24 N2 O3
FXVLEOBGAHQNAI-AVRDEDQJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.261 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.518α = 90
b = 65.518β = 90
c = 115.517γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-06-15 
  • Released Date: 2020-04-22 
  • 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: 2020-04-22
    Type: Initial release