Structure of TR-beta bound to selective thyromimetic GC-1

Experimental Data Snapshot

  • Resolution: 2.55 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

Starting Model: experimental
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Structural basis of GC-1 selectivity for thyroid hormone receptor isoforms.

Bleicher, L.Aparicio, R.Nunes, F.M.Martinez, L.Gomes Dias, S.M.Figueira, A.C.M.Santos, M.A.M.Venturelli, W.H.da Silva, R.Donate, P.M.Neves, F.A.Simeoni, L.A.Baxter, J.D.Webb, P.Skaf, M.S.Polikarpov, I.

(2008) BMC Struct Biol 8: 1-13

  • DOI: https://doi.org/10.1186/1472-6807-8-8
  • Primary Citation of Related Structures:  
    3HZF, 3ILZ, 3IMY

  • PubMed Abstract: 

    Thyroid receptors, TRalpha and TRbeta, are involved in important physiological functions such as metabolism, cholesterol level and heart activities. Whereas metabolism increase and cholesterol level lowering could be achieved by TRbeta isoform activation, TRalpha activation affects heart rates. Therefore, beta-selective thyromimetics have been developed as promising drug-candidates for treatment of obesity and elevated cholesterol level. GC-1 [3,5-dimethyl-4-(4'-hydroxy-3'-isopropylbenzyl)-phenoxy acetic acid] has ability to lower LDL cholesterol with 600- to 1400-fold more potency and approximately two- to threefold more efficacy than atorvastatin (Lipitor(c)) in studies in rats, mice and monkeys. To investigate GC-1 specificity, we solved crystal structures and performed molecular dynamics simulations of both isoforms complexed with GC-1. Crystal structures reveal that, in TRalpha Arg228 is observed in multiple conformations, an effect triggered by the differences in the interactions between GC-1 and Ser277 or the corresponding asparagine (Asn331) of TRbeta. The corresponding Arg282 of TRbeta is observed in only one single stable conformation, interacting effectively with the ligand. Molecular dynamics support this model: our simulations show that the multiple conformations can be observed for the Arg228 in TRalpha, in which the ligand interacts either strongly with the ligand or with the Ser277 residue. In contrast, a single stable Arg282 conformation is observed for TRbeta, in which it strongly interacts with both GC-1 and the Asn331. Our analysis suggests that the key factors for GC-1 selectivity are the presence of an oxyacetic acid ester oxygen and the absence of the amino group relative to T3. These results shed light into the beta-selectivity of GC-1 and may assist the development of new compounds with potential as drug candidates to the treatment of hypercholesterolemia and obesity.

  • Organizational Affiliation

    Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense, 400 CEP 13560-970 São Carlos, SP, Brazil. lbleicher@if.sc.usp.br

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thyroid hormone receptor beta261Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P10828 (Homo sapiens)
Explore P10828 
Go to UniProtKB:  P10828
GTEx:  ENSG00000151090 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10828
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on B72

Download Ideal Coordinates CCD File 
B [auth A]{4-[4-hydroxy-3-(1-methylethyl)benzyl]-3,5-dimethylphenoxy}acetic acid
C20 H24 O4
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on CAS
Binding Affinity Annotations 
IDSourceBinding Affinity
B72 BindingDB:  3IMY Ki: 0.32 (nM) from 1 assay(s)
Kd: min: 0.07, max: 0.2 (nM) from 3 assay(s)
EC50: min: 2.82, max: 18 (nM) from 3 assay(s)
PDBBind:  3IMY Kd: 0.2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.55 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.996α = 90
b = 68.996β = 90
c = 130.861γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MAR345dtbdata collection

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description