2ZXZ | pdb_00002zxz

Crystal structure of the human RXR alpha ligand binding domain bound to a synthetic agonist compound and a coactivator peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.278 (Depositor) 
  • R-Value Work: 
    0.206 (Depositor) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Silicon analogues of the RXR-selective retinoid agonist SR11237 (BMS649): chemistry and biology

Lippert, W.P.Burschka, C.Gotz, K.Kaupp, M.Ivanova, D.Gaudon, C.Sato, Y.Antony, P.Rochel, N.Moras, D.Gronemeyer, H.Tacke, R.

(2009) ChemMedChem 4: 1143-1152

  • DOI: https://doi.org/10.1002/cmdc.200900090
  • Primary Citation Related Structures: 
    2ZXZ, 2ZY0

  • PubMed Abstract: 

    C/Si switch: Twofold sila-substitution (C/Si exchange) in the RXR-selective retinoids 4 a (SR11237) and 5 a leads to 4 b (disila-SR11237) and 5 b, respectively. Chemistry and biology of the C/Si pairs are reported.SR11237 (BMS649, 4 a) is a pan-RXR-selective retinoid agonist. Its silicon analogue, disila-SR11237 (4 b; twofold C/Si exchange), was prepared in a multistep synthesis by starting from 1,2-bis(ethynyldimethylsilyl)ethane. In addition, the related C/Si analogues 5 a and 5 b, with an indane (disila-indane) instead of a tetraline (disila-tetraline) skeleton, were synthesized. The C/Si pairs 4 a/4 b and 5 a/5 b were studied for their interaction with retinoid receptors and were demonstrated to be highly potent RXR-selective ("rexinoid") agonists. Interestingly, twofold C/Si exchange in the indane moiety of 5 a resulted in a 10-fold increase in biological activity of the corresponding silicon-containing rexinoid 5 b, possibly resulting from an increased receptor affinity or a divergent allosteric effect on co-regulator-binding surfaces. The crystal structures of the ternary complexes formed by 5 a and 5 b, respectively, with the ligand-binding domain of hRXRalpha and a peptide of the co-activator TIF2/GRIP1 revealed additional interactions of the disila analogue 5 b with the H7 and H11 residues, supporting the first option of increased binding affinity. This is the first demonstration of an increase in binding affinity of a ligand to a nuclear receptor by C/Si replacement, thereby adding this C/Si switch strategy to the repertoire of nuclear receptor ligand design.


  • Organizational Affiliation
    • Universität Würzburg, Institut für Anorganische Chemie, Am Hubland, 97074 Würzburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 28.8 kDa 
  • Atom Count: 1,826 
  • Modeled Residue Count: 224 
  • Deposited Residue Count: 253 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alpha240Homo sapiensMutation(s): 0 
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
GRIP1 from Nuclear receptor coactivator 213N/AMutation(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
P26

Query on P26



Download:Ideal Coordinates CCD File
C [auth A]4-[2-(1,1,3,3-tetramethyl-2,3-dihydro-1H-inden-5-yl)-1,3-dioxolan-2-yl]benzoic acid
C23 H26 O4
ISZBCQLHSNHWLM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.278 (Depositor) 
  • R-Value Work:  0.206 (Depositor) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.079α = 90
b = 64.079β = 90
c = 110.389γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Advisory, Refinement description
  • Version 1.3: 2023-11-01
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description