5JY3 | pdb_00005jy3

CRYSTAL STRUCTURE OF LXRbeta (NUCLEAR RECEPTOR SUBFAMILY 1, GROUP H, MEMBER 2) COMPLEXED WITH BMS-852927


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.268 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5JY3

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of Highly Potent Liver X Receptor beta Agonists.

Kick, E.K.Busch, B.B.Martin, R.Stevens, W.C.Bollu, V.Xie, Y.Boren, B.C.Nyman, M.C.Nanao, M.H.Nguyen, L.Plonowski, A.Schulman, I.G.Yan, G.Zhang, H.Hou, X.Valente, M.N.Narayanan, R.Behnia, K.Rodrigues, A.D.Brock, B.Smalley, J.Cantor, G.H.Lupisella, J.Sleph, P.Grimm, D.Ostrowski, J.Wexler, R.R.Kirchgessner, T.Mohan, R.

(2016) ACS Med Chem Lett 7: 1207-1212

  • DOI: https://doi.org/10.1021/acsmedchemlett.6b00234
  • Primary Citation Related Structures: 
    5JY3

  • PubMed Abstract: 

    Introducing a uniquely substituted phenyl sulfone into a series of biphenyl imidazole liver X receptor (LXR) agonists afforded a dramatic potency improvement for induction of ATP binding cassette transporters, ABCA1 and ABCG1, in human whole blood. The agonist series demonstrated robust LXRβ activity (>70%) with low partial LXRα agonist activity (<25%) in cell assays, providing a window between desired blood cell ABCG1 gene induction in cynomolgus monkeys and modest elevation of plasma triglycerides for agonist 15 . The addition of polarity to the phenyl sulfone also reduced binding to the plasma protein, human α-1-acid glycoprotein. Agonist 15 was selected for clinical development based on the favorable combination of in vitro properties, excellent pharmacokinetic parameters, and a favorable lipid profile.


  • Organizational Affiliation
    • Department of Discovery Chemistry, Department of Cardiovascular Biology, Pharmaceutical Candidate Optimization, Research & Development, Bristol-Myers Squibb , P.O. Box 5400, Princeton, New Jersey 08543-5400, United States.

Macromolecule Content 

  • Total Structure Weight: 124.79 kDa 
  • Atom Count: 7,798 
  • Modeled Residue Count: 916 
  • Deposited Residue Count: 1,056 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Oxysterols receptor LXR-beta
A, B, C, D
264Homo sapiensMutation(s): 0 
Gene Names: NR1H2LXRBNERUNR
UniProt & NIH Common Fund Data Resources
Find proteins for P55055 (Homo sapiens)
Explore P55055 
Go to UniProtKB:  P55055
PHAROS:  P55055
GTEx:  ENSG00000131408 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55055
Sequence Annotations
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
6OX BindingDB:  5JY3 Ki: 12 (nM) from 1 assay(s)
EC50: min: 0.6, max: 24 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.268 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.66α = 90
b = 120.35β = 107.49
c = 55.72γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2017-01-04
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations, Structure summary