8RW8 | pdb_00008rw8

Brain and muscle ARNT-like 1 (BMAL1) PAS-B domain in-complex with core circadian modulator (CCM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 
    0.228 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Pharmacological targeting of BMAL1 modulates circadian and immune pathways.

Pu, H.Bailey, L.C.Bauer, L.G.Voronkov, M.Baxter, M.Huber, K.V.M.Khorasanizadeh, S.Ray, D.Rastinejad, F.

(2025) Nat Chem Biol 21: 736-745

  • DOI: https://doi.org/10.1038/s41589-025-01863-x
  • Primary Citation of Related Structures:  
    8RW6, 8RW8

  • PubMed Abstract: 

    The basic helix-loop-helix PER-ARNT-SIM (bHLH-PAS) proteins BMAL1 and CLOCK heterodimerize to form the master transcription factor governing rhythmic gene expression. Owing to connections between circadian regulation and numerous physiological pathways, targeting the BMAL1-CLOCK complex pharmacologically is an attractive entry point for intervening in circadian-related processes. In this study, we developed a small molecule, Core Circadian Modulator (CCM), that targets the cavity in the PASB domain of BMAL1, causing it to expand, leading to conformational changes in the PASB domain and altering the functions of BMAL1 as a transcription factor. Biochemical, structural and cellular investigations validate the high level of selectivity of CCM in engaging BMAL1, enabling direct access to BMAL1-CLOCK cellular activities. CCM induces dose-dependent alterations in PER2-Luc oscillations and orchestrates the downregulation of inflammatory and phagocytic pathways in macrophages. These findings collectively reveal that the BMAL1 protein architecture is inherently configured to enable the binding of chemical ligands for functional modulation.


  • Organizational Affiliation
    • Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Basic helix-loop-helix ARNT-like protein 1A [auth B]114Homo sapiensMutation(s): 0 
Gene Names: BMAL1ARNTLBHLHE5MOP3PASD3
UniProt & NIH Common Fund Data Resources
Find proteins for O00327 (Homo sapiens)
Explore O00327 
Go to UniProtKB:  O00327
PHAROS:  O00327
GTEx:  ENSG00000133794 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00327
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H3Q (Subject of Investigation/LOI)
Query on A1H3Q

Download Ideal Coordinates CCD File 
C [auth B](2~{R})-3-[(4-ethyl-1-benzofuran-7-yl)oxy]-2-fluoranyl-propan-1-ol
C13 H15 F O3
JHNOWMZIFWNJQX-SNVBAGLBSA-N
A1H3P (Subject of Investigation/LOI)
Query on A1H3P

Download Ideal Coordinates CCD File 
B
(2~{S})-3-[(4-ethyl-1-benzofuran-7-yl)oxy]-2-fluoranyl-propan-1-ol
C13 H15 F O3
JHNOWMZIFWNJQX-JTQLQIEISA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free:  0.228 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.57α = 90
b = 39.83β = 90
c = 73.34γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom210664/Z/18/Z

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Database references
  • Version 1.2: 2025-05-07
    Changes: Database references