5AVL

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.198 

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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:  
    5AVI, 5AVL

  • 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 domain and the ligands, two key functional groups were introduced ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Oxysterols receptor LXR-alphaA283Homo sapiensMutation(s): 0 
Gene Names: NR1H3, LXRA
UniProt & NIH Common Fund Data Resources
Find proteins for Q13133 (Homo sapiens)
Explore Q13133 
Go to UniProtKB:  Q13133
PHAROS:  Q13133
GTEx:  ENSG00000025434 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13133
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor coactivator 1B25Homo sapiensMutation(s): 0 
Gene Names: NCOA1, BHLHE74, SRC1
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
PHAROS:  Q15788
GTEx:  ENSG00000084676 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15788
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4KQ
Query on 4KQ
Download Ideal Coordinates CCD File 
C [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
4KQ BindingDB:  5AVL EC50: 510 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.198 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.909α = 90
b = 124.909β = 90
c = 91.92γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata collection
SCALEPACKdata scaling
CNSphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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