9D8U | pdb_00009d8u

Crystal structure of CDK6 in complex with atirmociclib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.253 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
View more details

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
Cyclin-dependent kinase 6307Homo sapiensMutation(s): 0 
Gene Names: CDK6CDKN6
EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q00534 (Homo sapiens)
Explore Q00534 
Go to UniProtKB:  Q00534
PHAROS:  Q00534
GTEx:  ENSG00000105810 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00534
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AZ4 (Subject of Investigation/LOI)
Query on A1AZ4

Download Ideal Coordinates CCD File 
B [auth A]Atirmociclib
C22 H27 Cl F N5 O3
QYJLBHRAPDJOSO-NVXWUHKLSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.253 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.1α = 90
b = 102.1β = 90
c = 59.9γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction
autoBUSTERphasing

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


Funding OrganizationLocationGrant Number
Not fundedUnited States--

Revision History  (Full details and data files)

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