9CSK | pdb_00009csk

Crystal structure of CDK4 cyclin D1 in complex with atirmociclib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.270 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1AZ4Click on this verticalbar to view details

This is version 1.0 of the entry. See complete history


Literature

CDK4 selective inhibition improves preclinical anti-tumor efficacy and safety.

Palmer, C.L.Boras, B.Pascual, B.Li, N.Li, D.Garza, S.Huser, N.Yuan, J.T.Cianfrogna, J.A.Sung, T.McMillan, E.Wei, N.Carmody, J.Kang, A.N.Darensburg, S.Dodd, T.Oakley, J.V.Solowiej, J.Nguyen, L.Orr, S.T.M.Chen, P.Johnson, E.Yu, X.Diehl, W.C.Gallego, G.M.Jalaie, M.Ferre, R.A.Cho-Schultz, S.Shen, H.Deal, J.G.Zhang, Q.Baffi, T.R.Xu, M.Roh, W.Lapira-Miller, J.Goudeau, J.Yu, Y.Gupta, R.Kim, K.Dann, S.G.Kan, Z.Kath, J.C.Nair, S.K.Miller, N.Murray, B.W.Nager, A.R.Quinlan, C.Petroski, M.D.Zhang, C.Sacaan, A.VanArsdale, T.Anders, L.

(2025) Cancer Cell 43: 464-481.e14

  • DOI: https://doi.org/10.1016/j.ccell.2025.02.006
  • Primary Citation of Related Structures:  
    9CSK, 9D8U

  • PubMed Abstract: 

    CDK4/6 inhibitors have revolutionized treatment of hormone receptor positive (HR+), HER2 non-amplified (HER2-) breast cancer. Yet, all "dual" CDK4/6 inhibitors show common dose-limiting hematologic toxicities, foremost neutropenia. This poses challenges to provide these agents at concentrations necessary to extinguish cell cycling in tumors. HR+ breast cancer cells are highly dependent on CDK4 but not CDK6. By contrast, CDK4 is dispensable for human bone marrow derived cells, due to the primary and compensatory role of CDK6 in hematopoiesis. This prompted us to develop atirmociclib (PF-07220060), a next-generation CDK4 selective inhibitor. Atirmociclib's impact on circulating neutrophils was reduced, in proportion with its increase in CDK4 versus CDK6 selectivity. Realized dose intensification led to greater CDK4 inhibition and deeper anti-tumor responses, pointing to CDK4 target coverage as a limiting factor of CDK4/6 inhibitor efficacy. We also highlight combinatorial agents that may counter acquired resistance to CDK4 selective inhibition and widen its clinical application.


  • Organizational Affiliation

    Pfizer Global Research and Development La Jolla, 10770 Science Center Drive, San Diego, CA 92121, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
G1/S-specific cyclin-D1
A, C
257Homo sapiensMutation(s): 0 
Gene Names: CCND1BCL1PRAD1
UniProt & NIH Common Fund Data Resources
Find proteins for P24385 (Homo sapiens)
Explore P24385 
Go to UniProtKB:  P24385
PHAROS:  P24385
GTEx:  ENSG00000110092 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24385
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 4
B, D
314Homo sapiensMutation(s): 2 
Gene Names: CDK4
EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for P11802 (Homo sapiens)
Explore P11802 
Go to UniProtKB:  P11802
PHAROS:  P11802
GTEx:  ENSG00000135446 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11802
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.270 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.511α = 90
b = 64.289β = 91.67
c = 186.208γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1AZ4Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data

  • Released Date: 2025-03-26 
  • Deposition Author(s): Johnson, E.

Funding OrganizationLocationGrant Number
Not fundedUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release