3JZC

Crystal Structure of TR-beta bound to the selective thyromimetic TRIAC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Gaining ligand selectivity in thyroid hormone receptors via entropy.

Martinez, L.Nascimento, A.S.Nunes, F.M.Phillips, K.Aparicio, R.Dias, S.M.Figueira, A.C.Lin, J.H.Nguyen, P.Apriletti, J.W.Neves, F.A.Baxter, J.D.Webb, P.Skaf, M.S.Polikarpov, I.

(2009) Proc.Natl.Acad.Sci.USA 106: 20717-20722

  • DOI: 10.1073/pnas.0911024106
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nuclear receptors are important targets for pharmaceuticals, but similarities between family members cause difficulties in obtaining highly selective compounds. Synthetic ligands that are selective for thyroid hormone (TH) receptor beta (TRbeta) vs. ...

    Nuclear receptors are important targets for pharmaceuticals, but similarities between family members cause difficulties in obtaining highly selective compounds. Synthetic ligands that are selective for thyroid hormone (TH) receptor beta (TRbeta) vs. TRalpha reduce cholesterol and fat without effects on heart rate; thus, it is important to understand TRbeta-selective binding. Binding of 3 selective ligands (GC-1, KB141, and GC-24) is characterized at the atomic level; preferential binding depends on a nonconserved residue (Asn-331beta) in the TRbeta ligand-binding cavity (LBC), and GC-24 gains extra selectivity from insertion of a bulky side group into an extension of the LBC that only opens up with this ligand. Here we report that the natural TH 3,5,3'-triodothyroacetic acid (Triac) exhibits a previously unrecognized mechanism of TRbeta selectivity. TR x-ray structures reveal better fit of ligand with the TRalpha LBC. The TRbeta LBC, however, expands relative to TRalpha in the presence of Triac (549 A(3) vs. 461 A(3)), and molecular dynamics simulations reveal that water occupies the extra space. Increased solvation compensates for weaker interactions of ligand with TRbeta and permits greater flexibility of the Triac carboxylate group in TRbeta than in TRalpha. We propose that this effect results in lower entropic restraint and decreases free energy of interactions between Triac and TRbeta, explaining subtype-selective binding. Similar effects could potentially be exploited in nuclear receptor drug design.


    Organizational Affiliation

    Instituto de QuĂ­mica, Universidade Estadual de Campinas, SP 13084-862, Campinas, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thyroid hormone receptor beta
A
263Homo sapiensMutation(s): 0 
Gene Names: THRB (ERBA2, NR1A2, THR1)
Find proteins for P10828 (Homo sapiens)
Go to Gene View: THRB
Go to UniProtKB:  P10828
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4HY
Query on 4HY

Download SDF File 
Download CCD File 
A
[4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID
C14 H9 I3 O4
UOWZUVNAGUAEQC-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAS
Query on CAS
A
L-PEPTIDE LINKINGC5 H12 As N O2 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4HYIC50: 0 - 0.1 nM (100) BINDINGDB
4HYIC50: ~1 nM BINDINGMOAD
4HYIC50: 2.94 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.198 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 68.781α = 90.00
b = 68.781β = 90.00
c = 131.013γ = 120.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOSFLMdata reduction
MOLREPphasing
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance