5AVI

Crystal structure of LXRalpha in complex with tert-butyl benzoate analog, compound 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 

wwPDB Validation 3D Report Full Report



Literature

Discovery and structure-guided optimization of tert-butyl 6-(phenoxymethyl)-3-(trifluoromethyl)benzoates as liver X receptor agonists

Matsui, Y.Yamaguchi, T.Yamazaki, T.Yoshida, M.Arai, M.Terasaka, N.Honzumi, S.Wakabayashi, K.Hayashi, S.Nakai, D.Hanzawa, H.Tamaki, K.

(2015) Bioorg Med Chem Lett 25: 3914-3920

  • DOI: 10.1016/j.bmcl.2015.07.047
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • To obtain potent liver X receptor (LXR) agonists, a structure-activity relationship study was performed on a series of tert-butyl benzoate analogs. As the crystal structure analysis suggested applicable interactions between the LXR ligand-binding dom ...

    To obtain potent liver X receptor (LXR) agonists, a structure-activity relationship study was performed on a series of tert-butyl benzoate analogs. As the crystal structure analysis suggested applicable interactions between the LXR ligand-binding domain and the ligands, two key functional groups were introduced. The introduction of the hydroxyl group on the C6-position of the benzoate part enhanced the agonistic activity in a cell-based assay, and the carboxyl group in terminal improved the pharmacokinetic profile in mice, respectively. The obtained compound 32b increased blood ABCA1 mRNA expression without plasma TG elevation in both mice and cynomolgus monkeys.


    Organizational Affiliation

    R&D Division, Daiichi Sankyo Co., Ltd, 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan. Electronic address: tamaki.kazuhiko.s2@daiichisankyo.co.jp.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oxysterols receptor LXR-alpha
A, C
283Homo sapiensMutation(s): 0 
Gene Names: NR1H3LXRA
Find proteins for Q13133 (Homo sapiens)
Go to UniProtKB:  Q13133
NIH Common Fund Data Resources
PHAROS  Q13133

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 1
B, D
25Homo sapiensMutation(s): 0 
Gene Names: NCOA1BHLHE74SRC1
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS  Q15788
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4KM
Query on 4KM

Download CCD File 
A, C
tert-butyl 2-[[4-[ethanoyl(methyl)amino]phenoxy]methyl]-5-(trifluoromethyl)benzoate
C22 H24 F3 N O4
YZWZMPWHXSZLBQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4KMEC50:  310   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.356α = 90
b = 124.356β = 90
c = 91.916γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata collection
SCALEPACKdata scaling
CNSphasing
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-26
    Type: Initial release