9IX5 | pdb_00009ix5

An agonist(compound 15n) of Thyroid Hormone Receptor B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 
    0.277 (Depositor), 0.274 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Discovery of a Potent, Selective, and Multiple His435 Mutation-Sensitive Thyroid Hormone Receptor beta Agonist.

Li, Q.Yao, B.Zhao, S.Lu, Z.Wu, X.Lu, Z.Wu, T.Li, J.Chen, X.Chen, Z.Zhang, C.Wu, D.Zhang, Y.Xiang, Q.Li, Y.Xu, Y.

(2025) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00164
  • Primary Citation of Related Structures:  
    9IX5, 9J0K

  • PubMed Abstract: 

    Beyond selectivity concerns for thyroid hormone receptor β (THR-β) agonists, intolerance to the His435 mutation remains a challenge. Following our previous study, we performed detailed modifications on the 7-position of isoquinoline, specifically targeting the hydrophobic region of the THR-β ligand-binding pocket (LBP). This led to the identification of compound 15n , which showed potent THR-β agonistic activity (EC 50 : 3.2 nM), moderately selectivity (∼10-fold), and good activation of multiple His435 mutants (EC 50 : 134.2 nM to 515.5 nM). Co-crystal structures revealed that the introduction of small-volume groups into the hydrophobic pocket of THR-β almost did not significantly displace helix 11 or helix 3, explaining why 15n can activate multiple His435 mutants simultaneously. Multiple experiments confirmed that 15n exhibits excellent lipid metabolism, safety, and pharmacokinetic properties. Together, 15n emerges as a potent, selective, and His435 mutation-sensitive THR-β agonist, offering potential for treating dyslipidemia, metabolic dysfunction-associated steatohepatitis (MASH), or resistance to thyroid hormone (RTH).


  • Organizational Affiliation

    China-New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thyroid hormone receptor beta259Homo sapiensMutation(s): 0 
Gene Names: THRBERBA2NR1A2THR1
UniProt & NIH Common Fund Data Resources
Find proteins for P10828 (Homo sapiens)
Explore P10828 
Go to UniProtKB:  P10828
PHAROS:  P10828
GTEx:  ENSG00000151090 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10828
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 212Homo sapiensMutation(s): 0 
Gene Names: NCOA2BHLHE75SRC2TIF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EAC (Subject of Investigation/LOI)
Query on A1EAC

Download Ideal Coordinates CCD File 
C [auth A]2-[(1-methoxy-7-naphthalen-2-yloxy-4-oxidanyl-isoquinolin-3-yl)carbonylamino]ethanoic acid
C23 H18 N2 O6
OJFUTFNCRATZLZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.277 (Depositor), 0.274 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.577α = 90
b = 107.577β = 90
c = 57.103γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2025-07-02 
  • Deposition Author(s): Yao, B., Li, Y.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82173745

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release