8UV0

Discovery of (4-Pyrazolyl)-2-Aminopyrimidines as Potent and Selective Inhibitors of Cyclin-Dependent Kinase 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.155 

Starting Model: experimental
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Literature

Discovery of (4-Pyrazolyl)-2-aminopyrimidines as Potent and Selective Inhibitors of Cyclin-Dependent Kinase 2.

Hummel, J.R.Xiao, K.J.Yang, J.C.Epling, L.B.Mukai, K.Ye, Q.Xu, M.Qian, D.Huo, L.Weber, M.Roman, V.Lo, Y.Drake, K.Stump, K.Covington, M.Kapilashrami, K.Zhang, G.Ye, M.Diamond, S.Yeleswaram, S.Macarron, R.Deller, M.C.Wee, S.Kim, S.Wang, X.Wu, L.Yao, W.

(2024) J Med Chem 67: 3112-3126

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c02287
  • Primary Citation of Related Structures:  
    8UV0

  • PubMed Abstract: 

    CDK2 is a critical regulator of the cell cycle. For a variety of human cancers, the dysregulation of CDK2/cyclin E1 can lead to tumor growth and proliferation. Historically, early efforts to develop CDK2 inhibitors with clinical applications proved unsuccessful due to challenges in achieving selectivity over off-target CDK isoforms with associated toxicity. In this report, we describe the discovery of (4-pyrazolyl)-2-aminopyrimidines as a potent class of CDK2 inhibitors that display selectivity over CDKs 1, 4, 6, 7, and 9. SAR studies led to the identification of compound 17 , a kinase selective and highly potent CDK2 inhibitor (IC 50 = 0.29 nM). The evaluation of 17 in CCNE1 -amplified mouse models shows the pharmacodynamic inhibition of CDK2, measured by reduced Rb phosphorylation, and antitumor activity.


  • Organizational Affiliation

    Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware 19803, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 2297Homo 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
XKU (Subject of Investigation/LOI)
Query on XKU

Download Ideal Coordinates CCD File 
B [auth A]1-{(4M)-4-[2-{[1-(cyclopropanesulfonyl)piperidin-4-yl]amino}-5-(trifluoromethyl)pyrimidin-4-yl]-1H-pyrazol-1-yl}-2-methylpropan-2-ol
C20 H27 F3 N6 O3 S
HTBKVAJZYRVZSW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.663α = 90
b = 72.009β = 90
c = 71.913γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
STARANISOdata scaling
DIMPLEphasing

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: 2024-02-14
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Database references