4M8H | pdb_00004m8h

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.265 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1016/j.bmc.2013.11.039
  • Primary Citation Related Structures: 
    4M8E, 4M8H

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 27.61 kDa 
  • Atom Count: 1,937 
  • Modeled Residue Count: 225 
  • Deposited Residue Count: 242 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alpha231Homo sapiensMutation(s): 0 
Gene Names: NR2B1RXRA
UniProt & NIH Common Fund Data Resources
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
PHAROS:  P19793
GTEx:  ENSG00000186350 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19793
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 211Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R4M

Query on R4M



Download:Ideal Coordinates CCD File
C [auth A](2E,6Z,8E)-3,7-dimethyl-8-[(4R)-4-methyl-3,4-dihydronaphthalen-1(2H)-ylidene]octa-2,6-dienoic acid
C21 H26 O2
ONGGGDPVQXADCB-RGZUUTACSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.265 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.92α = 90
b = 65.92β = 90
c = 111.65γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-22
    Type: Initial release
  • Version 1.1: 2022-08-17
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-09-20
    Changes: Data collection, Refinement description