Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 36175.03 
• Atom Count: 1995 
• Residue Count: 308 
• 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)


• 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: 2.8 Å
• R-Value Free: 0.243 
• R-Value Work: 0.192 

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


• 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: 

Daiichi Sankyo RD Novare Co., Ltd, 1-16-13, Kita-Kasai, Edogawa-ku, Tokyo 134-8630, Japan. Electronic address: [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Oxysterols receptor LXR-alpha	A	283	Homo sapiens	Mutation(s): 0  Gene Names: NR1H3 (LXRA)
Find proteins for Q13133 (Homo sapiens) Go to Gene View: NR1H3 Go to UniProtKB:  Q13133

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
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) Go to Gene View: NCOA1 Go to UniProtKB:  Q15788

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
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 (100) BINDINGDB

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 = 124.909	α = 90.00
b = 124.909	β = 90.00
c = 91.920	γ = 90.00

Software Package:

Software Name	Purpose
CNS	phasing
PDB_EXTRACT	data extraction
REFMAC	refinement
SCALEPACK	data scaling
DENZO	data collection
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