1Q4X

Crystal Structure of Human Thyroid Hormone Receptor beta LBD in complex with specific agonist GC-24


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Ligand selectivity by seeking hydrophobicity in thyroid hormone receptor.

Borngraeber, S.Budny, M.J.Chiellini, G.Cunha-Lima, S.T.Togashi, M.Webb, P.Baxter, J.D.Scanlan, T.S.Fletterick, R.J.

(2003) Proc.Natl.Acad.Sci.USA 100: 15358-15363

  • DOI: 10.1073/pnas.2136689100

  • PubMed Abstract: 
  • Selective therapeutics for nuclear receptors would revolutionize treatment for endocrine disease. Specific control of nuclear receptor activity is challenging because the internal cavities that bind hormones can be virtually identical. Only one highl ...

    Selective therapeutics for nuclear receptors would revolutionize treatment for endocrine disease. Specific control of nuclear receptor activity is challenging because the internal cavities that bind hormones can be virtually identical. Only one highly selective hormone analog is known for the thyroid receptor, GC-24, an agonist for human thyroid hormone receptor beta. The compound differs from natural hormone in benzyl, substituting for an iodine atom in the 3' position. The benzyl is too large to fit into the enclosed pocket of the receptor. The crystal structure of human thyroid hormone receptor beta at 2.8-A resolution with GC-24 bound explains its agonist activity and unique isoform specificity. The benzyl of GC-24 is accommodated through shifts of 3-4 A in two helices. These helices are required for binding hormone and positioning the critical helix 12 at the C terminus. Despite these changes, the complex associates with coactivator as tightly as human thyroid hormone receptor bound to thyroid hormone and is fully active. Our data suggest that increased specificity of ligand recognition derives from creating a new hydrophobic cluster with ligand and protein components.


    Organizational Affiliation

    Department of Biochemistry/Biophysics, University of California, San Francisco, CA 94143-2240, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thyroid hormone receptor beta-1
A
253Homo sapiensGene 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
G24
Query on G24

Download SDF File 
Download CCD File 
A
[4-(3-BENZYL-4-HYDROXYBENZYL)-3,5-DIMETHYLPHENOXY]ACETIC ACID
GC-24
C24 H24 O4
JYHIGYLGYNCMGI-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
G24Kd: 0.33 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.216 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 56.570α = 90.00
b = 56.570β = 90.00
c = 390.050γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-02-03
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance