8BUL

Structure of DDB1 bound to DS11-engaged CDK12-cyclin K

  • Classification: LIGASE
  • Organism(s): Homo sapiens
  • Expression System: Trichoplusia ni
  • Mutation(s): No 

  • Deposited: 2022-11-30 Released: 2023-09-13 
  • Deposition Author(s): Kozicka, Z., Kempf, G., Petzold, G., Thoma, N.H.
  • Funding Organization(s): European Research Council (ERC), Swiss National Science Foundation, Swiss Cancer League, Marie Sklodowska-Curie Actions, FragNET ITN, Other private

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Design principles for cyclin K molecular glue degraders.

Kozicka, Z.Suchyta, D.J.Focht, V.Kempf, G.Petzold, G.Jentzsch, M.Zou, C.Di Genua, C.Donovan, K.A.Coomar, S.Cigler, M.Mayor-Ruiz, C.Schmid-Burgk, J.L.Haussinger, D.Winter, G.E.Fischer, E.S.Slabicki, M.Gillingham, D.Ebert, B.L.Thoma, N.H.

(2024) Nat Chem Biol 20: 93-102

  • DOI: https://doi.org/10.1038/s41589-023-01409-z
  • Primary Citation of Related Structures:  
    8BU1, 8BU2, 8BU3, 8BU5, 8BU7, 8BUA, 8BUB, 8BUD, 8BUE, 8BUF, 8BUI, 8BUJ, 8BUK, 8BUL, 8BUM, 8BUN, 8BUO, 8BUP

  • PubMed Abstract: 

    Molecular glue degraders are an effective therapeutic modality, but their design principles are not well understood. Recently, several unexpectedly diverse compounds were reported to deplete cyclin K by linking CDK12-cyclin K to the DDB1-CUL4-RBX1 E3 ligase. Here, to investigate how chemically dissimilar small molecules trigger cyclin K degradation, we evaluated 91 candidate degraders in structural, biophysical and cellular studies and reveal all compounds acquire glue activity via simultaneous CDK12 binding and engagement of DDB1 interfacial residues, in particular Arg928. While we identify multiple published kinase inhibitors as cryptic degraders, we also show that these glues do not require pronounced inhibitory properties for activity and that the relative degree of CDK12 inhibition versus cyclin K degradation is tuneable. We further demonstrate cyclin K degraders have transcriptional signatures distinct from CDK12 inhibitors, thereby offering unique therapeutic opportunities. The systematic structure-activity relationship analysis presented herein provides a conceptual framework for rational molecular glue design.


  • Organizational Affiliation

    Institute of Clinical Chemistry and Clinical Pharmacology, University and University Hospital Bonn, Bonn, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
GTEx:  ENSG00000167986 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16531
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 12
B, E, H
344Homo sapiensMutation(s): 0 
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
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
GTEx:  ENSG00000090061 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75909
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RSU (Subject of Investigation/LOI)
Query on RSU

Download Ideal Coordinates CCD File 
HA [auth H],
P [auth B],
Y [auth E]
(2~{R})-2-[[6-(3-phenylpropylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol
C21 H30 N6 O
HXKIFNLNVMCGAG-QGZVFWFLSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
CA [auth F]
DA [auth G]
EA [auth G]
AA [auth F],
BA [auth F],
CA [auth F],
DA [auth G],
EA [auth G],
FA [auth G],
GA [auth G],
IA [auth H],
JA [auth H],
K [auth A],
KA [auth I],
L [auth A],
LA [auth I],
M [auth A],
MA [auth I],
N [auth A],
O [auth A],
Q [auth C],
R [auth C],
S [auth C],
U [auth D],
V [auth D],
W [auth D],
X [auth D],
Z [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
J [auth A],
T [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
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: 3.40 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 249.356α = 90
b = 249.356β = 90
c = 217.993γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Cootmodel building
STARANISOdata scaling
autoPROCdata processing
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union666068
Swiss National Science FoundationSwitzerland31003A_179541
Swiss National Science FoundationSwitzerland310030_301206
Swiss Cancer LeagueSwitzerland4980-02-2020
Swiss National Science FoundationSwitzerlandCRSII5_186230
Marie Sklodowska-Curie Actions, FragNET ITNEuropean Union765445
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-13
    Type: Initial release
  • Version 1.1: 2024-01-03
    Changes: Database references