9D0U | pdb_00009d0u

Crystal structure of CDK2 in complex with Cpd 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.260 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

CDK2 heterobifunctional degraders co-degrade CDK2 and cyclin E resulting in efficacy in CCNE1-amplified and overexpressed cancers.

Kwiatkowski, N.Liang, T.Sha, Z.Collier, P.N.Yang, A.Sathappa, M.Paul, A.Su, L.Zheng, X.Aversa, R.Li, K.Mehovic, R.Kolodzy, C.Breitkopf, S.B.Chen, D.Howarth, C.L.Yuan, K.Jo, H.Growney, J.D.Weiss, M.Williams, J.

(2025) Cell Chem Biol 32: 556-569.e24

  • DOI: https://doi.org/10.1016/j.chembiol.2025.03.006
  • Primary Citation of Related Structures:  
    9D0U, 9D0V, 9D0W, 9D0X

  • PubMed Abstract: 

    CCNE1 amplification drives aberrant CDK2-cyclin E1 activity in cancer. Despite activity of CDK2 inhibitors, their therapeutic margins are limited by poor CDK selectivity. We developed a degrader with high selectivity for CDK2 over CDK1 that also unexpectedly led to cyclin E1 degradation and potent and complete suppression of RB phosphorylation at concentrations with low CDK2 occupancy and negligible CDK1 degradation. Co-depletion of CDK2 and cyclin E1 also resensitized palbociclib-adapted breast cancer cells to cell cycle blockade. Overall, the improved potency and selectivity of the degrader for CDK2 over small-molecule inhibitors drives antiproliferative activity with greater specificity for CCNE1 amp cancer cells and RB dependency. Using an orally administered degrader, we demonstrate deep and sustained RB pathway suppression, which is needed to induce stasis in CCNE1 amp tumors. These results highlight the potential of this modality to target CDK2 potently and selectivity in this biomarker-defined patient population with high unmet need.


  • Organizational Affiliation
    • Kymera Therapeutics, Inc., Biological Sciences, 500 North Beacon St. 4th Floor, Watertown, MA 02472, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 2298Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
PHAROS:  P24941
GTEx:  ENSG00000123374 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24941
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A1H (Subject of Investigation/LOI)
Query on A1A1H

Download Ideal Coordinates CCD File 
B [auth A]6-chloro-8-cyclopentyl-2-[4-(ethanesulfonyl)-2-methylanilino]pyrido[2,3-d]pyrimidin-7(8H)-one
C21 H23 Cl N4 O3 S
KTADOXGSNAXMOO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.260 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.72α = 90
b = 71.68β = 90
c = 72.19γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Database references