5YSO

Crystal structure of Estrogen Related Receptor-3 (ERR-gamma) ligand binding domain with DN200434

• PDB DOI: https://doi.org/10.2210/pdb5YSO/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-11-14 Released: 2018-12-26 
• Deposition Author(s): Cho, S.J., Chin, J.W., Yoon, H.S., Jeon, Y.H., Bae, J.H., Song, J.Y.
• Funding Organization(s): the korea health industry development institute

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.243 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 

Literature

A Novel Orally Active Inverse Agonist of Estrogen-related Receptor Gamma (ERR gamma ), DN200434, A Booster of NIS in Anaplastic Thyroid Cancer.

Singh, T.D., Song, J., Kim, J., Chin, J., Ji, H.D., Lee, J.E., Lee, S.B., Yoon, H., Yu, J.H., Kim, S.K., Yoon, G.S., Hwang, H., Lee, H.W., Oh, J.M., Lee, S.W., Lee, J., Choi, H.S., Na, S.Y., Choi, W.I., Park, Y.J., Song, Y.S., Kim, Y.A., Lee, I.K., Cho, S.J., Jeon, Y.H.

(2019) Clin Cancer Res 25: 5069-5081

• PubMed: 31010838 
• DOI: https://doi.org/10.1158/1078-0432.CCR-18-3007
• Primary Citation of Related Structures:  
  5YSO


• PubMed Abstract: 
  

  New strategies to restore sodium iodide symporter (NIS) expression and function in radioiodine therapy-refractive anaplastic thyroid cancers (ATCs) are urgently required. Recently, we reported the regulatory role of estrogen-related receptor gamma (ERRγ) in ATC cell NIS function. Herein, we identified DN200434 as a highly potent (functional IC ₅₀ = 0.006 μmol/L), selective, and orally available ERRγ inverse agonist for NIS enhancement in ATC.

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Organizational Affiliation: 

Department of Medical Oncology Laboratory, All India Institute of Medical Sciences (AIIMS), New Delhi, India.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 82.4 kDa 
• Atom Count: 5,355 
• Modelled Residue Count: 650 
• Deposited Residue Count: 714 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen-related receptor gamma	A, B, C	238	Homo sapiens	Mutation(s): 0  Gene Names: ESRRG, ERR3, ERRG2, KIAA0832, NR3B3
UniProt & NIH Common Fund Data Resources
Find proteins for P62508 (Homo sapiens) Explore P62508  Go to UniProtKB:  P62508
PHAROS:  P62508 GTEx:  ENSG00000196482

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
90C	D [auth A], E [auth B], F [auth C]	4-[5-oxidanyl-2-phenyl-1-[4-(4-propan-2-ylpiperazin-1-yl)phenyl]pent-1-enyl]phenol C30 H36 N2 O2 RUUIHSHMHGOGMZ-QVIHXGFCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.243 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.886	α = 90
b = 79.828	β = 107.81
c = 106.714	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
PHENIX	phasing
HKL-2000	data scaling
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-12-26 
Deposition Author(s): Cho, S.J., Chin, J.W., Yoon, H.S., Jeon, Y.H., Bae, J.H., Song, J.Y.

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Funding Organization	Location	Grant Number
the korea health industry development institute	Korea, Republic Of	HI16C1501

Revision History  

• Version 1.0: 2018-12-26
  Type: Initial release
  
• Version 1.1: 2019-05-01
  Changes: Data collection, Database references
• Version 1.2: 2019-08-28
  Changes: Data collection, Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description