8D8I

Crystal structure of Reverb alpha in complex with synthetic agonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

Starting Model: other
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural basis of synthetic agonist activation of the nuclear receptor REV-ERB.

Murray, M.H.Valfort, A.C.Koelblen, T.Ronin, C.Ciesielski, F.Chatterjee, A.Veerakanellore, G.B.Elgendy, B.Walker, J.K.Hegazy, L.Burris, T.P.

(2022) Nat Commun 13: 7131-7131

  • DOI: https://doi.org/10.1038/s41467-022-34892-4
  • Primary Citation of Related Structures:  
    8D8I

  • PubMed Abstract: 

    The nuclear receptor REV-ERB plays an important role in a range of physiological processes. REV-ERB behaves as a ligand-dependent transcriptional repressor and heme has been identified as a physiological agonist. Our current understanding of how ligands bind to and regulate transcriptional repression by REV-ERB is based on the structure of heme bound to REV-ERB. However, porphyrin (heme) analogues have been avoided as a source of synthetic agonists due to the wide range of heme binding proteins and potential pleotropic effects. How non-porphyrin synthetic agonists bind to and regulate REV-ERB has not yet been defined. Here, we characterize a high affinity synthetic REV-ERB agonist, STL1267, and describe its mechanism of binding to REV-ERB as well as the method by which it recruits transcriptional corepressor both of which are unique and distinct from that of heme-bound REV-ERB.


  • Organizational Affiliation

    Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor subfamily 1 group D member 1237Homo sapiensMutation(s): 0 
Gene Names: NR1D1EAR1HREVTHRAL
UniProt & NIH Common Fund Data Resources
Find proteins for P20393 (Homo sapiens)
Explore P20393 
Go to UniProtKB:  P20393
PHAROS:  P20393
GTEx:  ENSG00000126368 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20393
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor corepressor 120Homo sapiensMutation(s): 1 
Gene Names: NCOR1KIAA1047
UniProt & NIH Common Fund Data Resources
Find proteins for O75376 (Homo sapiens)
Explore O75376 
Go to UniProtKB:  O75376
PHAROS:  O75376
GTEx:  ENSG00000141027 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75376
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QFX (Subject of Investigation/LOI)
Query on QFX

Download Ideal Coordinates CCD File 
C [auth A](4S)-6-[([1,1'-biphenyl]-2-yl)oxy]-3-chloro[1,2,4]triazolo[4,3-b]pyridazine
C17 H11 Cl N4 O
XWHTYUYQMHCFMT-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.073α = 90
b = 115.073β = 90
c = 107.32γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata processing
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedW81XWH-19-1-0632

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Data collection, Refinement description