Crystal structure of Estrogen-related Receptor-3 (ERR-gamma) ligand binding domain with DN201000

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Discovery of Potent, Selective, and Orally Bioavailable Estrogen-Related Receptor-gamma Inverse Agonists To Restore the Sodium Iodide Symporter Function in Anaplastic Thyroid Cancer.

Kim, J.Song, J.Ji, H.D.Yoo, E.K.Lee, J.E.Lee, S.B.Oh, J.M.Lee, S.Hwang, J.S.Yoon, H.Kim, D.S.Lee, S.J.Jeong, M.Lee, S.Kim, K.H.Choi, H.S.Lee, S.W.Park, K.G.Lee, I.K.Kim, S.H.Hwang, H.Jeon, Y.H.Chin, J.Cho, S.J.

(2019) J Med Chem 62: 1837-1858

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01296
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    An inverse agonist of estrogen-related receptor-γ (ERRγ), an orphan nuclear receptor encoded by E srrg, enhances sodium iodide symporter-mediated radioiodine uptake in anaplastic thyroid cancer (ATC) cells, thereby facilitating responsiveness to radioiodine therapy in vitro. We synthesized potent, selective, and orally bioavailable ERRγ-inverse agonists and evaluated their activity by analyzing in vitro pharmacology and absorption, distribution, metabolism, excretion, and toxicity profiles. X-ray crystallographic analysis of the ligand and ERRγ complex showed that 35 completely binds to the target protein (PDB 6A6K ). Our results showed improved radioiodine avidity in ATC cells through compound 35-mediated upregulation of iodide-handling genes, leading to enhanced responsiveness to radioiodine therapy in vitro. Importantly, in vivo 124 I-positron emission tomography/computed tomography imaging revealed that 35 increases radioiodine avidity in CAL62 tumors. Collectively, these results demonstrated that 35 can be developed as a promising treatment for ERRγ-related cancer in the future.

  • Organizational Affiliation

    New Drug Development Center , Daegu-Gyeongbuk Medical Innovation Foundation , Daegu 41061 , South Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen-related receptor gamma
A, B, C
238Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62508 (Homo sapiens)
Explore P62508 
Go to UniProtKB:  P62508
PHAROS:  P62508
GTEx:  ENSG00000196482 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62508
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 9S6

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]
C30 H36 N2 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.828α = 90
b = 78.571β = 109.19
c = 106.963γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description