3FC6

hRXRalpha & mLXRalpha with an indole Pharmacophore, SB786875

• PDB DOI: https://doi.org/10.2210/pdb3FC6/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens, Mus musculus
• Mutation(s): No 


• Deposited: 2008-11-21 Released: 2009-02-10 
• Deposition Author(s): Washburn, D.G., Hoang, T.H., Campobasso, N., Smallwood, A., Parks, D.J., Webb, C.L., Frank, K., Nord, M., Duraiswami, C., Evans, C., Jaye, M., Thompson, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.250 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Literature

Synthesis and SAR of potent LXR agonists containing an indole pharmacophore.

Washburn, D.G., Hoang, T.H., Campobasso, N., Smallwood, A., Parks, D.J., Webb, C.L., Frank, K.A., Nord, M., Duraiswami, C., Evans, C., Jaye, M., Thompson, S.K.

(2009) Bioorg Med Chem Lett 19: 1097-1100

• PubMed: 19167885 
• DOI: https://doi.org/10.1016/j.bmcl.2009.01.004
• Primary Citation of Related Structures:  
  3FC6


• PubMed Abstract: 
  

  A novel series of 1H-indol-1-yl tertiary amine LXR agonists has been designed. Compounds from this series were potent agonists with good rat pharmacokinetic parameters. In addition, the crystal structure of an LXR agonist bound to LXRalpha will be disclosed.

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Organizational Affiliation: 

Department of Chemistry, Molecular Discovery Research, GlaxoSmithKline Pharmaceuticals, 709 Swedeland Road, King of Prussia, PA 19406, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 117.31 kDa 
• Atom Count: 7,497 
• Modelled Residue Count: 891 
• Deposited Residue Count: 1,016 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoic acid receptor RXR-alpha	A, C	242	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P19793 (Homo sapiens) Explore P19793  Go to UniProtKB:  P19793
PHAROS:  P19793 GTEx:  ENSG00000186350

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nr1h3 protein	B, D	266	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Z0Y9 (Mus musculus) Explore Q9Z0Y9  Go to UniProtKB:  Q9Z0Y9
IMPC:  MGI:1352462

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LX2	F [auth B], H [auth D]	[4-(3-{[2-chloro-3-(trifluoromethyl)benzyl](2,2-diphenylethyl)amino}propoxy)-1H-indol-1-yl]acetic acid C35 H32 Cl F3 N2 O3 RHWNXOWPCIQOAH-UHFFFAOYSA-N
REA	E [auth A], G [auth C]	RETINOIC ACID C20 H28 O2 SHGAZHPCJJPHSC-YCNIQYBTSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
REA	BindingDB:  3FC6	IC50: min: 5.00e+4, max: 5.00e+4 (nM) from 3 assay(s)
LX2	BindingDB:  3FC6	EC50: 14 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.250 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.162	α = 90
b = 90.029	β = 111.92
c = 101.642	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MLPHARE	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-10 
Deposition Author(s): Washburn, D.G., Hoang, T.H., Campobasso, N., Smallwood, A., Parks, D.J., Webb, C.L., Frank, K., Nord, M., Duraiswami, C., Evans, C., Jaye, M., Thompson, S.K.

Revision History  

• Version 1.0: 2009-02-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations