4PP5

Crystal structure of human Retinoid X Receptor alpha-ligand binding domain complex with 5-methyl UAB30 and the coactivator peptide GRIP-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/jm5004792
  • Primary Citation of Related Structures:  
    4POH, 4POJ, 4PP3, 4PP5

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alpha231Homo sapiensMutation(s): 0 
Gene Names: NR2B1RXRARXRA NR2B1
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 213Homo 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
2W0
Query on 2W0

Download Ideal Coordinates CCD File 
C [auth A](2E,4E,6Z,8E)-3,7-dimethyl-8-(5-methyl-3,4-dihydronaphthalen-1(2H)-ylidene)octa-2,4,6-trienoic acid
C21 H24 O2
PUNLLTFBKSEJRJ-MLZXBFFUSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
2W0 BindingDB:  4PP5 Kd: min: 18, max: 2240 (nM) from 2 assay(s)
EC50: min: 440, max: 720 (nM) from 2 assay(s)
Binding MOAD:  4PP5 Kd: 18 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.37α = 90
b = 66.37β = 90
c = 111.431γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
d*TREKdata reduction
d*TREKdata 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: 2014-06-18
    Type: Initial release
  • Version 1.1: 2014-07-23
    Changes: Database references
  • Version 1.2: 2022-08-17
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-02-28
    Changes: Data collection