6TD3

Structure of DDB1 bound to CR8-engaged CDK12-cyclinK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.46 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

Starting Models: experimental
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This is version 1.3 of the entry. See complete history


Literature

The CDK inhibitor CR8 acts as a molecular glue degrader that depletes cyclin K.

Slabicki, M.Kozicka, Z.Petzold, G.Li, Y.D.Manojkumar, M.Bunker, R.D.Donovan, K.A.Sievers, Q.L.Koeppel, J.Suchyta, D.Sperling, A.S.Fink, E.C.Gasser, J.A.Wang, L.R.Corsello, S.M.Sellar, R.S.Jan, M.Gillingham, D.Scholl, C.Frohling, S.Golub, T.R.Fischer, E.S.Thoma, N.H.Ebert, B.L.

(2020) Nature 585: 293-297

  • DOI: https://doi.org/10.1038/s41586-020-2374-x
  • Primary Citation of Related Structures:  
    6TD3

  • PubMed Abstract: 

    Molecular glue compounds induce protein-protein interactions that, in the context of a ubiquitin ligase, lead to protein degradation 1 . Unlike traditional enzyme inhibitors, these molecular glue degraders act substoichiometrically to catalyse the rapid depletion of previously inaccessible targets 2 . They are clinically effective and highly sought-after, but have thus far only been discovered serendipitously. Here, through systematically mining databases for correlations between the cytotoxicity of 4,518 clinical and preclinical small molecules and the expression levels of E3 ligase components across hundreds of human cancer cell lines 3-5 , we identify CR8-a cyclin-dependent kinase (CDK) inhibitor 6 -as a compound that acts as a molecular glue degrader. The CDK-bound form of CR8 has a solvent-exposed pyridyl moiety that induces the formation of a complex between CDK12-cyclin K and the CUL4 adaptor protein DDB1, bypassing the requirement for a substrate receptor and presenting cyclin K for ubiquitination and degradation. Our studies demonstrate that chemical alteration of surface-exposed moieties can confer gain-of-function glue properties to an inhibitor, and we propose this as a broader strategy through which target-binding molecules could be converted into molecular glues.


  • Organizational Affiliation

    Broad Institute of MIT and Harvard, Cambridge, MA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage-binding protein 1
A, D, G
840Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens)
Explore Q16531 
Go to UniProtKB:  Q16531
PHAROS:  Q16531
GTEx:  ENSG00000167986 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16531
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 12
B, E, H
344Homo sapiensMutation(s): 1 
Gene Names: CDK12CRK7CRKRSKIAA0904
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYV4 (Homo sapiens)
Explore Q9NYV4 
Go to UniProtKB:  Q9NYV4
PHAROS:  Q9NYV4
GTEx:  ENSG00000167258 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NYV4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-K
C, F, I
271Homo sapiensMutation(s): 0 
Gene Names: CCNKCPR4
UniProt & NIH Common Fund Data Resources
Find proteins for O75909 (Homo sapiens)
Explore O75909 
Go to UniProtKB:  O75909
PHAROS:  O75909
GTEx:  ENSG00000090061 
Entity Groups  
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UniProt GroupO75909
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
B, E, H
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.46 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 250.749α = 90
b = 250.749β = 90
c = 217.92γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
DIALSdata reduction
STARANISOdata scaling
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilSwitzerland666068

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Source and taxonomy, Structure summary
  • Version 1.3: 2024-01-24
    Changes: Refinement description