4M8E

CRYSTAL STRUCTURE OF HUMAN RETINOID X RECEPTOR ALPHA-LIGAND BINDING DOMAIN COMPLEX WITH (S) 4-Methyl 9cUAB30 COACTIVATOR PEPTIDE GRIP-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Methyl-substituted conformationally constrained rexinoid agonists for the retinoid X receptors demonstrate improved efficacy for cancer therapy and prevention.

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

(2014) Bioorg.Med.Chem. 22: 178-185

  • DOI: 10.1016/j.bmc.2013.11.039
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • (2E,4E,6Z,8Z)-8-(3',4'-Dihydro-1'(2H)-naphthalen-1'-ylidene)-3,7-dimethyl-2,3,6-octatrienoinic acid, 9cUAB30, is a selective rexinoid for the retinoid X nuclear receptors (RXR). 9cUAB30 displays substantial chemopreventive capacity with little toxici ...

    (2E,4E,6Z,8Z)-8-(3',4'-Dihydro-1'(2H)-naphthalen-1'-ylidene)-3,7-dimethyl-2,3,6-octatrienoinic acid, 9cUAB30, is a selective rexinoid for the retinoid X nuclear receptors (RXR). 9cUAB30 displays substantial chemopreventive capacity with little toxicity and is being translated to the clinic as a novel cancer prevention agent. To improve on the potency of 9cUAB30, we synthesized 4-methyl analogs of 9cUAB30, which introduced chirality at the 4-position of the tetralone ring. The syntheses and biological evaluations of the racemic homolog and enantiomers are reported. We demonstrate that the S-enantiomer is the most potent and least toxic even though these enantiomers bind in a similar conformation in the ligand binding domain of RXR.


    Organizational Affiliation

    Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA. Electronic address: wbrou@uab.edu.,Department of Surgery, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Department of Vision Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Department of Surgical Oncology, University of Illinois, Chicago, IL 60612, USA.,Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA. Electronic address: muccio@uab.edu.,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.




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
11Homo 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
29V
Query on 29V

Download SDF File 
Download CCD File 
A
(3E,6Z,8E)-3,7-dimethyl-8-[(4S)-4-methyl-3,4-dihydronaphthalen-1(2H)-ylidene]octa-3,6-dienoic acid
C21 H26 O2
AAFLIKIWMRJTLU-JOVHMOHQSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
29VKd: 13 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.208 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 66.279α = 90.00
b = 66.279β = 90.00
c = 111.011γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CNSrefinement
HKL-2000data collection
PDB_EXTRACTdata extraction
CNSphasing
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-22
    Type: Initial release