4RME

Crystal structure of human Retinoid X receptor alpha ligand binding domain complex with 9cUAB111 and coactivator peptide GRIP-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Conformationally Defined Rexinoids and Their Efficacy in the Prevention of Mammary Cancers.

Atigadda, V.R.Xia, G.Deshpande, A.Wu, L.Kedishvili, N.Smith, C.D.Krontiras, H.Bland, K.I.Grubbs, C.J.Brouillette, W.J.Muccio, D.D.

(2015) J.Med.Chem. 58: 7763-7774

  • DOI: 10.1021/acs.jmedchem.5b00829
  • 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 (UAB30) is currently undergoing clinical evaluation as a novel cancer prevention agent. In efforts to develop even more highly potent rexinoids that p ...

    (2E,4E,6Z,8Z)-8-(3',4'-Dihydro-1'(2H)-naphthalen-1'-ylidene)-3,7-dimethyl-2,3,6-octatrienoinic acid (UAB30) is currently undergoing clinical evaluation as a novel cancer prevention agent. In efforts to develop even more highly potent rexinoids that prevent breast cancer without toxicity, we further explore here the structure-activity relationship of two separate classes of rexinoids. UAB30 belongs to the class II rexinoids and possesses a 9Z-tetraenoic acid chain bonded to a tetralone ring, whereas the class I rexinoids contain the same 9Z-tetraenoic acid chain bonded to a disubstituted cyclohexenyl ring. Among the 12 class I and class II rexinoids evaluated, the class I rexinoid 11 is most effective in preventing breast cancers in an in vivo rat model alone or in combination with tamoxifen. Rexinoid 11 also reduces the size of established tumors and exhibits a therapeutic effect. However, 11 induces hypertriglyceridemia at its effective dose. On the other hand rexinoid 10 does not increase triglyceride levels while being effective in the in vivo chemoprevention assay. X-ray studies of four rexinoids bound to the ligand binding domain of the retinoid X receptor reveal key structural aspects that enhance potency as well as those that enhance the synthesis of lipids.


    Organizational Affiliation

    Departments of †Chemistry, ‡Biochemistry and Molecular Genetics, §Vision Sciences, and ∥Surgery, 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
235Homo 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
3T2
Query on 3T2

Download SDF File 
Download CCD File 
A
(2E,4E,6Z,8E)-3,7-dimethyl-8-[2-(3-methylbutyl)-3-(propan-2-yl)cyclohex-2-en-1-ylidene]octa-2,4,6-trienoic acid
C24 H36 O2
FMJPOOLCNCUSEB-QBSSGBIUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3T2Kd: 9 - 1210 nM (100) BINDINGDB
3T2EC50: 22 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.210 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 65.971α = 90.00
b = 65.971β = 90.00
c = 112.347γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
CNSphasing
HKL-2000data scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-10-21 
  • Released Date: 2015-09-16 
  • Deposition Author(s): Xia, G., Muccio, D.D.

Revision History 

  • Version 1.0: 2015-09-16
    Type: Initial release
  • Version 1.1: 2015-10-21
    Type: Database references