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


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 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


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

  • DOI: 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) ...

    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.


    Organizational Affiliation

    Daiichi Sankyo RD Novare Co., Ltd., 1-16-13 Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Steroid hormone receptor ERR1A,
C [auth B]
245Homo sapiensMutation(s): 0 
Gene Names: ESRRAERR1ESRL1NR3B1
UniProt & NIH Common Fund Data Resources
Find proteins for P11474 (Homo sapiens)
Explore P11474 
Go to UniProtKB:  P11474
PHAROS:  P11474
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11474
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma coactivator 1-alphaB [auth P],
D [auth Q]
12Homo sapiensMutation(s): 1 
Gene Names: PPARGC1ALEM6PGC1PGC1APPARGC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBK2 (Homo sapiens)
Explore Q9UBK2 
Go to UniProtKB:  Q9UBK2
PHAROS:  Q9UBK2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBK2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HVO (Subject of Investigation/LOI)
Query on HVO

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]
1-[4-(3-tert-butyl-4-oxidanyl-phenoxy)phenyl]ethanone
C18 H20 O3
WSVZSZVSZTYTCC-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD

Download Ideal Coordinates CCD File 
F [auth P]IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
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 = 71.326α = 90
b = 71.326β = 90
c = 97.653γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release