6KX8

Crystal structure of mouse Cryptochrome 2 in complex with TH301 compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Isoform-selective regulation of mammalian cryptochromes.

Miller, S.Son, Y.L.Aikawa, Y.Makino, E.Nagai, Y.Srivastava, A.Oshima, T.Sugiyama, A.Hara, A.Abe, K.Hirata, K.Oishi, S.Hagihara, S.Sato, A.Tama, F.Itami, K.Kay, S.A.Hatori, M.Hirota, T.

(2020) Nat Chem Biol 16: 676-685

  • DOI: https://doi.org/10.1038/s41589-020-0505-1
  • Primary Citation of Related Structures:  
    6KX4, 6KX5, 6KX6, 6KX7, 6KX8

  • PubMed Abstract: 

    CRY1 and CRY2 are essential components of the circadian clock controlling daily physiological rhythms. Accumulating evidences indicate distinct roles of these highly homologous proteins, in addition to redundant functions. Therefore, the development of isoform-selective compounds represents an effective approach towards understanding the similarities and differences of CRY1 and CRY2 by controlling each isoform individually. We conducted phenotypic screenings of circadian clock modulators, and identified KL101 and TH301 that selectively stabilize CRY1 and CRY2, respectively. Crystal structures of CRY-compound complexes revealed conservation of compound-binding sites between CRY1 and CRY2. We further discovered a unique mechanism underlying compound selectivity in which the disordered C-terminal region outside the pocket was required for the differential effects of KL101 and TH301 against CRY isoforms. By using these compounds, we found a new role of CRY1 and CRY2 as enhancers of brown adipocyte differentiation, providing the basis of CRY-mediated regulation of energy expenditure.


  • Organizational Affiliation

    Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cryptochrome-2
A, B
514Mus musculusMutation(s): 0 
Gene Names: Cry2
UniProt
Find proteins for Q9R194 (Mus musculus)
Explore Q9R194 
Go to UniProtKB:  Q9R194
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9R194
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DYX (Subject of Investigation/LOI)
Query on DYX

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
1-(4-chlorophenyl)-N-[2-(4-methoxyphenyl)-5,5-bis(oxidanylidene)-4,6-dihydrothieno[3,4-c]pyrazol-3-yl]cyclopentane-1-carboxamide
C24 H24 Cl N3 O4 S
DDCUCVXSGYHWRJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.171α = 90
b = 120.25β = 95.208
c = 69.392γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
MOSFLMdata reduction
DIALSdata scaling
xia2data scaling
PHASERphasing

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 ScienceJapan15H05590
Japan Society for the Promotion of ScienceJapan18H02402

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2020-04-15
    Changes: Database references
  • Version 1.2: 2020-06-03
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description