2PIN

Thyroid receptor beta in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insight into the mode of action of a direct inhibitor of coregulator binding to the thyroid hormone receptor.

Estebanez-Perpina, E.Arnold, L.A.Jouravel, N.Togashi, M.Blethrow, J.Mar, E.Nguyen, P.Phillips, K.J.Baxter, J.D.Webb, P.Guy, R.K.Fletterick, R.J.

(2007) Mol.Endocrinol. 21: 2919-2928

  • DOI: 10.1210/me.2007-0174

  • PubMed Abstract: 
  • The development of nuclear hormone receptor antagonists that directly inhibit the association of the receptor with its essential coactivators would allow useful manipulation of nuclear hormone receptor signaling. We previously identified 3-(dibutylam ...

    The development of nuclear hormone receptor antagonists that directly inhibit the association of the receptor with its essential coactivators would allow useful manipulation of nuclear hormone receptor signaling. We previously identified 3-(dibutylamino)-1-(4-hexylphenyl)-propan-1-one (DHPPA), an aromatic beta-amino ketone that inhibits coactivator recruitment to thyroid hormone receptor beta (TRbeta), in a high-throughput screen. Initial evidence suggested that the aromatic beta-enone 1-(4-hexylphenyl)-prop-2-en-1-one (HPPE), which alkylates a specific cysteine residue on the TRbeta surface, is liberated from DHPPA. Nevertheless, aspects of the mechanism and specificity of action of DHPPA remained unclear. Here, we report an x-ray structure of TRbeta with the inhibitor HPPE at 2.3-A resolution. Unreacted HPPE is located at the interface that normally mediates binding between TRbeta and its coactivator. Several lines of evidence, including experiments with TRbeta mutants and mass spectroscopic analysis, showed that HPPE specifically alkylates cysteine residue 298 of TRbeta, which is located near the activation function-2 pocket. We propose that this covalent adduct formation proceeds through a two-step mechanism: 1) beta-elimination to form HPPE; and 2) a covalent bond slowly forms between HPPE and TRbeta. DHPPA represents a novel class of potent TRbeta antagonist, and its crystal structure suggests new ways to design antagonists that target the assembly of nuclear hormone receptor gene-regulatory complexes and block transcription.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158-2240, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thyroid hormone receptor beta-1
A, B
253Homo sapiensMutation(s): 1 
Gene Names: THRB (ERBA2, NR1A2, THR1)
Find proteins for P10828 (Homo sapiens)
Go to Gene View: THRB
Go to UniProtKB:  P10828
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
LEG
Query on LEG

Download SDF File 
Download CCD File 
A, B
1-(4-HEXYLPHENYL)PROP-2-EN-1-ONE
C15 H20 O
IINHTEWASPUCMH-UHFFFAOYSA-N
 Ligand Interaction
4HY
Query on 4HY

Download SDF File 
Download CCD File 
A, B
[4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID
C14 H9 I3 O4
UOWZUVNAGUAEQC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4HYIC50: 0 - 0.1 nM (99) BINDINGDB
LEGIC50: 1500 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.130α = 90.00
b = 92.870β = 109.65
c = 58.350γ = 90.00
Software Package:
Software NamePurpose
ELVESdata reduction
SCALAdata scaling
CNSphasing
ELVESrefinement
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-18
    Type: Refinement description