5AVL

Crystal structure of LXRalpha in complex with tert-butyl benzoate analog, compound 32b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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
  • Primary Citation of Related Structures:  

  • 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

    Daiichi Sankyo RD Novare Co., Ltd, 1-16-13, Kita-Kasai, Edogawa-ku, Tokyo 134-8630, Japan. Electronic address: matsui.yumi.gk@rdn.daiichisankyo.co.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oxysterols receptor LXR-alpha
A
283Homo sapiensMutation(s): 0 
Gene Names: NR1H3 (LXRA)
Find proteins for Q13133 (Homo sapiens)
Go to Gene View: NR1H3
Go to UniProtKB:  Q13133
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 1
B
25Homo sapiensMutation(s): 0 
Gene Names: NCOA1 (BHLHE74, SRC1)
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to Gene View: NCOA1
Go to UniProtKB:  Q15788
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4KQ
Query on 4KQ

Download SDF File 
Download CCD File 
A
2-[4-[4-[[2-[(2-methylpropan-2-yl)oxycarbonyl]-3-oxidanyl-4-(trifluoromethyl)phenyl]methoxy]phenyl]phenyl]ethanoic acid
C27 H25 F3 O6
XWHRMVBUKJEZFY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.192 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 124.909α = 90.00
b = 124.909β = 90.00
c = 91.920γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
PDB_EXTRACTdata extraction
REFMACrefinement
SCALEPACKdata scaling
DENZOdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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