7D1C

Crystal structure of mouse Cryptochrome 1 in complex with compound TH303


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Photopharmacological Manipulation of Mammalian CRY1 for Regulation of the Circadian Clock.

Kolarski, D.Miller, S.Oshima, T.Nagai, Y.Aoki, Y.Kobauri, P.Srivastava, A.Sugiyama, A.Amaike, K.Sato, A.Tama, F.Szymanski, W.Feringa, B.L.Itami, K.Hirota, T.

(2021) J Am Chem Soc 143: 2078-2087

  • DOI: https://doi.org/10.1021/jacs.0c12280
  • Primary Citation of Related Structures:  
    7D19, 7D1C

  • PubMed Abstract: 

    CRY1 and CRY2 proteins are highly conserved components of the circadian clock that controls daily physiological rhythms. Disruption of CRY functions are related to many diseases, including circadian sleep phase disorder. Development of isoform-selective and spatiotemporally controllable tools will facilitate the understanding of shared and distinct functions of CRY1 and CRY2. Here, we developed CRY1-selective compounds that enable light-dependent manipulation of the circadian clock. From phenotypic chemical screening in human cells, we identified benzophenone derivatives that lengthened the circadian period. These compounds selectively interacted with the CRY1 photolyase homology region, resulting in activation of CRY1 but not CRY2. The benzophenone moiety rearranged a CRY1 region called the "lid loop" located outside of the compound-binding pocket and formed a unique interaction with Phe409 in the lid loop. Manipulation of this key interaction was achieved by rationally designed replacement of the benzophenone with a switchable azobenzene moiety whose cis-trans isomerization can be controlled by light. The metastable cis form exhibited sufficiently high half-life in aqueous solutions and structurally mimicked the benzophenone unit, enabling reversible period regulation over days by cellular irradiation with visible light. This study revealed an unprecedented role of the lid loop in CRY-compound interaction and paves the way for spatiotemporal regulation of CRY1 activity by photopharmacology for molecular understanding of CRY1-dependent functions in health and disease.


  • Organizational Affiliation

    Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Groningen 9747 AG, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cryptochrome-1498Mus musculusMutation(s): 0 
Gene Names: Cry1
UniProt & NIH Common Fund Data Resources
Find proteins for P97784 (Mus musculus)
Explore P97784 
Go to UniProtKB:  P97784
IMPC:  MGI:1270841
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP97784
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOF (Subject of Investigation/LOI)
Query on GOF

Download Ideal Coordinates CCD File 
B [auth A]N-[2-(4-methoxyphenyl)-5,5-bis(oxidanylidene)-4,6-dihydrothieno[3,4-c]pyrazol-3-yl]-4-(phenylcarbonyl)benzamide
C26 H21 N3 O5 S
FETYBXQBGAFWOV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.078α = 90
b = 79.148β = 90
c = 133.139γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
SCALAdata scaling
xia2data reduction
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanJPMJPR14LA
Japan Society for the Promotion of Science (JSPS)Japan18H02402

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release
  • Version 1.1: 2021-02-17
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description