1H9U

The structure of the human retinoid-X-receptor beta ligand binding domain in complex with the specific synthetic agonist LG100268


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.273 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Structural Basis for the Specificity of Retinoid-X Receptor-Selective Agonists: New Insights Into the Role of Helix H12

Love, J.D.Gooch, J.T.Benko, S.Li, C.Nagy, L.Chatterjee, V.K.K.Evans, R.M.Schwabe, J.W.R.

(2002) J Biol Chem 277: 11385

  • DOI: 10.1074/jbc.M110869200
  • Primary Citation of Related Structures:  
    1H9U

  • PubMed Abstract: 
  • Ligands that specifically target retinoid-X receptors (RXRs) are emerging as potentially powerful therapies for cancer, diabetes, and the lowering of circulatory cholesterol. To date, RXR has only been crystallized in the absence of ligand or with th ...

    Ligands that specifically target retinoid-X receptors (RXRs) are emerging as potentially powerful therapies for cancer, diabetes, and the lowering of circulatory cholesterol. To date, RXR has only been crystallized in the absence of ligand or with the promiscuous ligand 9-cis retinoic acid, which also activates retinoic acid receptors. Here we present the structure of hRXRbeta in complex with the RXR-specific agonist LG100268 (LG268). The structure clearly reveals why LG268 is specific for the RXR ligand binding pocket and will not activate retinoic acid receptors. Intriguingly, in the crystals, the C-terminal "activation" helix (AF-2/helix H12) is trapped in a novel position not seen in other nuclear receptor structures such that it does not cap the ligand binding cavity. Mammalian two-hybrid assays indicate that LG268 is unable to release co-repressors from RXR unless co-activators are also present. Together these findings suggest that RXR ligands may be inefficient at repositioning helix H12.


    Organizational Affiliation

    Medical Research Council, Laboratory of Molecular Biology, Cambridge, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RETINOID X RECEPTOR, BETAABCD224Homo sapiensMutation(s): 0 
Gene Names: RXRBNR2B2
Find proteins for P28702 (Homo sapiens)
Explore P28702 
Go to UniProtKB:  P28702
NIH Common Fund Data Resources
PHAROS  P28702
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LG2
Query on LG2

Download CCD File 
A, B, C, D
6-[1-(3,5,5,8,8-PENTAMETHYL-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)CYCLOPROPYL]PYRIDINE-3-CARBOXYLIC ACID
C24 H29 N O2
SLXTWXQUEZSSTJ-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download CCD File 
A, B, C, D
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LG2Ki:  3   nM  BindingDB
LG2Kd:  3   nM  BindingDB
LG2Ki:  13   nM  BindingDB
LG2EC50:  38   nM  BindingDB
LG2EC50:  40   nM  BindingDB
LG2IC50:  0   nM  BindingDB
LG2EC50:  11   nM  BindingDB
LG2EC50:  3   nM  BindingDB
LG2Ki:  20   nM  BindingDB
LG2EC50:  4   nM  BindingDB
LG2EC50:  17   nM  BindingDB
LG2Ki:  7.5   nM  BindingDB
LG2Ki:  75   nM  BindingDB
LG2Ki:  18   nM  BindingDB
LG2Ki:  3515   nM  BindingDB
LG2Kd:  3   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.273 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.886α = 90
b = 106.882β = 122.56
c = 100.587γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-04-03
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance