7E2E

Crystal structure of the Estrogen-Related Receptor alpha (ERRalpha) ligand-binding domain (LBD) in complex with an agonist DS45500853 and a PGC-1alpha peptide

• PDB DOI: https://doi.org/10.2210/pdb7E2E/pdb

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


• Deposited: 2021-02-05 Released: 2021-06-30 
• Deposition Author(s): Ito, S., Shinozuka, T., Kimura, T., Izumi, M., Wakabayashi, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.305 
• R-Value Work: 0.250 
• R-Value Observed: 0.256 

Literature

Discovery of a Novel Class of ERR alpha Agonists.

Shinozuka, T., Ito, S., Kimura, T., Izumi, M., Wakabayashi, K.

(2021) ACS Med Chem Lett 12: 817-821

• PubMed: 34055231 
• DOI: https://doi.org/10.1021/acsmedchemlett.1c00100
• Primary Citation of Related Structures:  
  7E2E


• PubMed Abstract: 
  

  A novel class of estrogen-related receptor α (ERRα) agonists has been discovered. A structure-activity relationship study of high-throughput screening hits 1 and 2 led to the discovery of benzimidazole 3d (DS20362725) and acetophenone analogue 5c (DS45500853). The X-ray crystal structure of the ERRα ligand-binding domain in complex with 5c and PGC-1α coactivator peptide revealed conformational changes in the ligand-binding pocket to accommodate 5c and the key interaction between the protein and ligand. Since both analogues avoided PPARγ transcriptional activity, they can be useful tool compounds for investigating biological ERRα functions.

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Organizational Affiliation: 

R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 57.27 kDa 
• Atom Count: 3,610 
• Modelled Residue Count: 456 
• Deposited Residue Count: 514 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Steroid hormone receptor ERR1	A, C [auth B]	245	Homo sapiens	Mutation(s): 0  Gene Names: ESRRA, ERR1, ESRL1, NR3B1
UniProt & NIH Common Fund Data Resources
Find proteins for P11474 (Homo sapiens) Explore P11474  Go to UniProtKB:  P11474
PHAROS:  P11474 GTEx:  ENSG00000173153

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma coactivator 1-alpha	B [auth P], D [auth Q]	12	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBK2 (Homo sapiens) Explore Q9UBK2  Go to UniProtKB:  Q9UBK2
PHAROS:  Q9UBK2 GTEx:  ENSG00000109819

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HVO (Subject of Investigation/LOI)	E [auth A], G [auth B]	1-[4-(3-tert-butyl-4-oxidanyl-phenoxy)phenyl]ethanone C18 H20 O3 WSVZSZVSZTYTCC-UHFFFAOYSA-N
IOD	F [auth P]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.305 
• R-Value Work: 0.250 
• R-Value Observed: 0.256 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.326	α = 90
b = 71.326	β = 90
c = 97.653	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-30 
Deposition Author(s): Ito, S., Shinozuka, T., Kimura, T., Izumi, M., Wakabayashi, K.

Revision History  

• Version 1.0: 2021-06-30
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description