9D0V | pdb_00009d0v

Crystal structure of CDK2/CyclinE1 in complex with Cpd 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 
    0.231 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9D0V

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 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.

Macromolecule Content 

  • Total Structure Weight: 68.29 kDa 
  • Atom Count: 4,873 
  • Modeled Residue Count: 574 
  • Deposited Residue Count: 584 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
G1/S-specific cyclin-E1286Homo sapiensMutation(s): 0 
Gene Names: CCNE1CCNE
UniProt & NIH Common Fund Data Resources
Find proteins for P24864 (Homo sapiens)
Explore P24864 
Go to UniProtKB:  P24864
PHAROS:  P24864
GTEx:  ENSG00000105173 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24864
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A1H
(Subject of Investigation/LOI)

Query on A1A1H



Download:Ideal Coordinates CCD File
C [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
PEG

Query on PEG



Download:Ideal Coordinates CCD File
D [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth B],
F [auth B],
G [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
H [auth B],
I [auth B],
J [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
SEP
Query on SEP
B
L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.39α = 90
b = 76.39β = 90
c = 257.96γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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