3FC6

hRXRalpha & mLXRalpha with an indole Pharmacophore, SB786875


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

    Department of Chemistry, Molecular Discovery Research, GlaxoSmithKline Pharmaceuticals, 709 Swedeland Road, King of Prussia, PA 19406, USA. dave.g.washburn@gsk.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alphaA, C242Homo sapiensMutation(s): 0 
Gene Names: RXRANR2B1
UniProt & NIH Common Fund Data Resources
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
PHAROS:  P19793
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19793
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nr1h3 proteinB, D266Mus musculusMutation(s): 0 
Gene Names: Nr1h3Lxra
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Z0Y9 (Mus musculus)
Explore Q9Z0Y9 
Go to UniProtKB:  Q9Z0Y9
IMPC:  MGI:1352462
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Z0Y9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LX2
Query on LX2

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
REA
Query on REA

Download Ideal Coordinates CCD File 
E [auth A],
G [auth C]
RETINOIC ACID
C20 H28 O2
SHGAZHPCJJPHSC-YCNIQYBTSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding 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 = 122.162α = 90
b = 90.029β = 111.92
c = 101.642γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MLPHAREphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance