Crystal structure of TR-alpha bound to T4 in a second site

Experimental Data Snapshot

  • Resolution: 2.05 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 2.0 of the entry. See complete history


Identification of a new hormone-binding site on the surface of thyroid hormone receptor.

Souza, P.C.Puhl, A.C.Martinez, L.Aparicio, R.Nascimento, A.S.Figueira, A.C.Nguyen, P.Webb, P.Skaf, M.S.Polikarpov, I.

(2014) Mol Endocrinol 28: 534-545

  • DOI: https://doi.org/10.1210/me.2013-1359
  • Primary Citation of Related Structures:  
    4LNW, 4LNX

  • PubMed Abstract: 

    Thyroid hormone receptors (TRs) are members of the nuclear receptor superfamily of ligand-activated transcription factors involved in cell differentiation, growth, and homeostasis. Although X-ray structures of many nuclear receptor ligand-binding domains (LBDs) reveal that the ligand binds within the hydrophobic core of the ligand-binding pocket, a few studies suggest the possibility of ligands binding to other sites. Here, we report a new x-ray crystallographic structure of TR-LBD that shows a second binding site for T3 and T4 located between H9, H10, and H11 of the TRα LBD surface. Statistical multiple sequence analysis, site-directed mutagenesis, and cell transactivation assays indicate that residues of the second binding site could be important for the TR function. We also conducted molecular dynamics simulations to investigate ligand mobility and ligand-protein interaction for T3 and T4 bound to this new TR surface-binding site. Extensive molecular dynamics simulations designed to compute ligand-protein dissociation constant indicate that the binding affinities to this surface site are of the order of the plasma and intracellular concentrations of the thyroid hormones, suggesting that ligands may bind to this new binding site under physiological conditions. Therefore, the second binding site could be useful as a new target site for drug design and could modulate selectively TR functions.

  • Organizational Affiliation

    Institute of Chemistry (P.C.T.S., L.M., R.A., M.S.S.), State University of Campinas-UNICAMP, Campinas, Sao Paulo, Brazil; Institute of Physics of São Carlos (A.C.P., A.S.N., P.W., I.P.), University of São Paulo-USP, São Carlos, Sao Paulo, Brazil; National Laboratory of Biosciences (A.C.M.F.), CNPEM, Campinas, Sao Paulo, Brazil; University of California Medical Center (P.N.), Diabetes Center, San Francisco, California; and Genomic Medicine (P.W.), Houston Methodist Research Institute, Houston, Texas.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thyroid hormone receptor alpha267Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P10827 (Homo sapiens)
Explore P10827 
Go to UniProtKB:  P10827
PHAROS:  P10827
GTEx:  ENSG00000126351 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10827
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on T44

Download Ideal Coordinates CCD File 
C15 H11 I4 N O4
Query on T3

Download Ideal Coordinates CCD File 
C15 H12 I3 N O4
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on CAS
Binding Affinity Annotations 
IDSourceBinding Affinity
T3 BindingDB:  4LNX Ki: min: 0.22, max: 2.33 (nM) from 4 assay(s)
Kd: min: 0.06, max: 0.17 (nM) from 4 assay(s)
IC50: min: 0.24, max: 3.2 (nM) from 2 assay(s)
EC50: min: 0.41, max: 10 (nM) from 8 assay(s)
T44 BindingDB:  4LNX EC50: 19 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.05 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.744α = 90
b = 80.924β = 90
c = 101.871γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345dtbdata collection

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-04-16
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations