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 13GK | pdb_000013gk

CDK2 in complex with INCB125496


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 
    0.209 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

Discovery of INCB127443: A Potent and Orally Available Inhibitor of Cyclin-Dependent Kinase 2.

Mukai, K., Smith, B.R., Ye, Q., Epling, L.B., Lai, C., Huo, L., Bowen, S., Drake, K., Kennedy, K., Boer, J., Zimmer, D., Zhang, W., Hansbury, M.J., Chand, S., Li, J., Zhang, G., Stump, K., Lo, Y., Favata, M., Yang, G., Covington, M., Deller, M.C., Macarron, R., Jackson, J., Mayes, P., Kim, S., Wang, X., Hummel, J.R., Wu, L., Yao, W.

(2026) J Med Chem 69: 23915-23946

  • DOI: https://doi.org/10.1021/acs.jmedchem.6c01506
  • Primary Citation Related Structures: 
    13GK

  • PubMed Abstract: 

    CDK2 is a critical regulator of cell-cycle progression and is an attractive therapeutic target for cancers characterized by dysregulated cyclin E1 signaling. Despite this biological rationale, CDK2 has historically been challenging to target due to the difficulty of achieving selectivity over related CDK isoforms, particularly CDK1, where off-target inhibition may limit the therapeutic window. Building on our previously reported (4-pyrazolyl)-2-aminopyrimidine series, we pursued a multiparameter optimization strategy aimed at improving selectivity for CDK2 over CDK1 while balancing pharmacokinetic and physicochemical properties. Computationally guided replacement of the pyrazole with an imidazole led to a (4-imidazolyl)-2-aminopyrimidine series and culminated in the discovery of INCB127443 (30), a potent and orally bioavailable CDK2 inhibitor. INCB127443 combined favorable selectivity over CDK1 with a relatively flat pharmacokinetic profile, supporting sustained projected CDK2 coverage while limiting potential CDK1 engagement. In vivo, INCB127443 demonstrated dose-dependent inhibition of Rb phosphorylation and antitumor efficacy in CCNE1-high ovarian cancer xenograft models.


  • Organizational Affiliation: 
    • Incyte Research Institute, Incyte Corporation, 1801 Augustine Cut-Off, Wilmington, Delaware19803, United States.

Macromolecule Content 

  • Total Structure Weight: 34.85 kDa 
  • Atom Count: 2,571 
  • Modeled Residue Count: 285 
  • Deposited Residue Count: 298 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 2298Homo sapiensMutation(s): 0 
Gene Names: CDK2, CDKN2
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.659α = 90
b = 71.935β = 90
c = 72.282γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
DIMPLEphasing

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: 2026-09-30
    Type: Initial release
  • Version 1.1: 2026-10-14
    Changes: Structure summary
  • Version 1.2: 2026-11-04
    Changes: Database references