3KFC

Complex Structure of LXR with an agonist

• PDB DOI:  https://doi.org/10.2210/pdb3KFC/pdb

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


• Deposited: 2009-10-27 Released: 2009-12-08 
• Deposition Author(s): Olland, A., Bernotas, R.C., Unwalla, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.284 
• R-Value Work: 0.238 
• R-Value Observed: 0.240 

Literature

4-(3-Aryloxyaryl)quinoline sulfones are potent liver X receptor agonists.

Bernotas, R.C., Singhaus, R.R., Kaufman, D.H., Travins, J.M., Ullrich, J.W., Unwalla, R., Quinet, E., Evans, M., Nambi, P., Olland, A., Kauppi, B., Wilhelmsson, A., Goos-Nilsson, A., Wrobel, J.

(2010) Bioorg Med Chem Lett 20: 209-212

• PubMed: 19932617 
• DOI: https://doi.org/10.1016/j.bmcl.2009.10.132
• Primary Citation of Related Structures:  
  3KFC


• PubMed Abstract: 
  

A series of 4-(3-aryloxyaryl)quinolines with sulfone substituents on the terminal aryl ring (7) was prepared as LXR agonists. High affinity LXR ligands with excellent agonist potency and efficacy in functional assays of LXR activity were identified. In general, these sulfone agonists were equal to or superior to previously described alcohol and amide analogs in terms of affinity, functional potency, and microsomal stability. Many of the sulfones had LXRbeta binding IC(50) values <10nM while the most potent compounds in an ABCA1 mRNA induction assay in J774 mouse cells had EC(50) values <10nM and were as efficacious as T0901317.

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Organizational Affiliation: 

Chemical Sciences, Wyeth Pharmaceuticals, 500 Arcola Road, Collegeville, PA 19426, USA. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 117.56 kDa 
• Atom Count: 7,304 
• Modelled Residue Count: 884 
• Deposited Residue Count: 1,012 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxysterols receptor LXR-beta	A, B, C, D	253	Homo sapiens	Mutation(s): 0  Gene Names: NR1H2, LXRB, NER, UNR
UniProt & NIH Common Fund Data Resources
Find proteins for P55055 (Homo sapiens) Explore P55055  Go to UniProtKB:  P55055
PHAROS:  P55055

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
61X	E [auth A], F [auth B], G [auth D]	4-{3-[3-(methylsulfonyl)phenoxy]phenyl}-8-(trifluoromethyl)quinoline C23 H16 F3 N O3 S DZEKZLIXNYUATR-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
61X	BindingDB:  3KFC	IC50: 40 (nM) from 1 assay(s)
	Binding MOAD:  3KFC	IC50: 2.8 (nM) from 1 assay(s)
	PDBBind:  3KFC	IC50: 2.8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.284 
• R-Value Work: 0.238 
• R-Value Observed: 0.240 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.993	α = 90
b = 99.286	β = 90
c = 174.962	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-08 
Deposition Author(s): Olland, A., Bernotas, R.C., Unwalla, R.

Revision History  

• Version 1.0: 2009-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance