4POH

Crystal structure of human Retinoid X Receptor alpha-ligand binding domain complex with 8-methyl UAB30 and the coactivator peptide GRIP-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Methyl substitution of a rexinoid agonist improves potency and reveals site of lipid toxicity.

Atigadda, V.R.Xia, G.Desphande, A.Boerma, L.J.Lobo-Ruppert, S.Grubbs, C.J.Smith, C.D.Brouillette, W.J.Muccio, D.D.

(2014) J.Med.Chem. 57: 5370-5380

  • DOI: 10.1021/jm5004792
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • (2E,4E,6Z,8E)-8-(3',4'-Dihydro-1'(2'H)-naphthalen-1'-ylidene)-3,7-dimethyl-2,4,6-octatrienoic acid, 9cUAB30, is a selective rexinoid that displays substantial chemopreventive capacity with little toxicity. 4-Methyl-UAB30, an analogue of 9cUAB30, is a ...

    (2E,4E,6Z,8E)-8-(3',4'-Dihydro-1'(2'H)-naphthalen-1'-ylidene)-3,7-dimethyl-2,4,6-octatrienoic acid, 9cUAB30, is a selective rexinoid that displays substantial chemopreventive capacity with little toxicity. 4-Methyl-UAB30, an analogue of 9cUAB30, is a potent RXR agonist but caused increased lipid biosynthesis unlike 9cUAB30. To evaluate how methyl substitution influenced potency and lipid biosynthesis, we synthesized four 9cUAB30 homologues with methyl substitutions at the 5-, 6-, 7-, or 8-position of the tetralone ring. The syntheses and biological evaluations of these new analogues are reported here along with the X-ray crystal structures of each homologue bound to the ligand binding domain of hRXRα. We demonstrate that each homologue of 9cUAB30 is a more potent agonist, but only the 7-methyl-9cUAB30 caused severe hyperlipidemia in rats. On the basis of the X-ray crystal structures of these new rexinoids and bexarotene (Targretin) bound to hRXRα-LBD, we reveal that each rexinoid, which induced hyperlipidemia, had methyl groups that interacted with helix 7 residues of the LBD.


    Organizational Affiliation

    Departments of †Chemistry, ‡Biochemistry and Molecular Genetics, §Medicine, and ∥Vision Sciences, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinoic acid receptor RXR-alpha
A
231Homo sapiensMutation(s): 0 
Gene Names: RXRA (NR2B1)
Find proteins for P19793 (Homo sapiens)
Go to Gene View: RXRA
Go to UniProtKB:  P19793
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 2
B
13Homo sapiensMutation(s): 0 
Gene Names: NCOA2 (BHLHE75, SRC2, TIF2)
Find proteins for Q15596 (Homo sapiens)
Go to Gene View: NCOA2
Go to UniProtKB:  Q15596
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2VR
Query on 2VR

Download SDF File 
Download CCD File 
A
(2E,4E,6Z,8E)-3,7-dimethyl-8-(8-methyl-3,4-dihydronaphthalen-1(2H)-ylidene)octa-2,4,6-trienoic acid
C21 H24 O2
BNDWDYJEHFQYFR-GYMMWQCESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2VRKd: 10 - 2330 nM (100) BINDINGDB
2VREC50: 620 - 880 nM (100) BINDINGDB
2VRKd: 10 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.216 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 66.250α = 90.00
b = 66.250β = 90.00
c = 110.670γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
CNSphasing
HKL-2000data collection
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2014-07-23
    Type: Database references