Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.18 kDa 
• Atom Count: 2041 
• Residue Count: 239 
• Unique protein chains: 2

5AVL

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

• DOI: 10.2210/pdb5AVL/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-06-17 Released: 2015-08-26 
• Deposition Author(s): Matsui, Y., Hanzawa, H., Tamaki, K.

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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 

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

• PubMed: 26238323 
• 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. 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.

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Organizational Affiliation: 

R&D Division, Daiichi Sankyo Co., Ltd, 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxysterols receptor LXR-alpha	A	283	Homo sapiens	Mutation(s): 0  Gene Names: NR1H3, LXRA
Find proteins for Q13133 (Homo sapiens) Explore Q13133  Go to UniProtKB:  Q13133
NIH Common Fund Data Resources
PHAROS:  Q13133 GTEx:  ENSG00000025434

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 1	B	25	Homo sapiens	Mutation(s): 0  Gene Names: NCOA1, BHLHE74, SRC1 EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens) Explore Q15788  Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS:  Q15788 GTEx:  ENSG00000084676

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4KQ	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
4KQ	EC50:  510   nM  BindingDB

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 = 124.909	α = 90
b = 124.909	β = 90
c = 91.92	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data collection
SCALEPACK	data scaling
CNS	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-06-17 
• Released Date: 2015-08-26 
Deposition Author(s): Matsui, Y., Hanzawa, H., Tamaki, K.

Revision History 

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