2ZY0 image
Deposition Date 2009-01-09
Release Date 2009-08-11
Last Version Date 2023-11-01
Entry Detail
PDB ID:
2ZY0
Keywords:
Title:
Crystal structure of the human RXR alpha ligand binding domain bound to a synthetic agonist compound and a coactivator peptide
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
(Taxon ID: )
Method Details:
Experimental Method:
Resolution:
2.90 Å
R-Value Free:
0.28
R-Value Work:
0.21
R-Value Observed:
0.22
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Retinoic acid receptor RXR-alpha
Gene (Uniprot):RXRA
Chain IDs:A, C
Chain Length:240
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:GRIP1 from Nuclear receptor coactivator 2
Gene (Uniprot):NCOA2
Chain IDs:B, D
Chain Length:13
Number of Molecules:2
Biological Source:
Ligand Molecules
Primary Citation
Silicon analogues of the RXR-selective retinoid agonist SR11237 (BMS649): chemistry and biology
Chemmedchem 4 1143 1152 (2009)
PMID: 19496083 DOI: 10.1002/cmdc.200900090

Abstact

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.

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Primary Citation of related structures