2J4A | pdb_00002j4a

Human Thyroid hormone receptor beta ligand binding domain in complex with KB131084

• PDB DOI: https://doi.org/10.2210/pdb2J4A/pdb

• Classification: RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-08-28 Released: 2007-09-25 
• Deposition Author(s): Farnegardh, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.273 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

Thyroid Receptor Ligands. 6. A High Affinity "Direct Antagonist" Selective for the Thyroid Hormone Receptor.

Koehler, K., Gordon, S., Brandt, P., Carlsson, B., Backsbro-Saedi, A., Apelqvist, T., Agback, P., Grover, G.J., Nelson, W., Grynfarb, M., Farnegardh, M., Rehnmark, S., Malm, J.

(2006) J Med Chem 49: 6635

• PubMed: 17154490 
• DOI: https://doi.org/10.1021/jm060521i
• Primary Citation of Related Structures:  
  2J4A


• PubMed Abstract: 
  

  A new high-affinity thyroid hormone antagonist 6 with druglike properties was designed and synthesized. The compound behaved as an antagonist in a cell transactivation assay, and in a first in vivo experiment in rats.

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Organizational Affiliation: 

Karo Bio AB, Novum, Huddinge SE-141 57, Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 29.01 kDa 
• Atom Count: 2,096 
• Modelled Residue Count: 251 
• Deposited Residue Count: 253 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THYROID HORMONE RECEPTOR BETA-1	A	253	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P10828 (Homo sapiens) Explore P10828  Go to UniProtKB:  P10828
PHAROS:  P10828 GTEx:  ENSG00000151090

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OEF	B [auth A]	3,5-DIBROMO-4-(3-ISOPROPYL-PHENOXY)BENZOIC ACID C18 H18 Br2 O4 DGODJDXDANWOEP-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OEF	BindingDB:  2J4A	IC50: min: 0.03, max: 0.11 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.273 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.212	α = 90
b = 107.422	β = 90
c = 67.208	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-25 
Deposition Author(s): Farnegardh, M.

Revision History  

• Version 1.0: 2007-09-25
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references, Other