9PE7 | pdb_00009pe7

CDK6 to CDK4 active site surrogate in complex with compound 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.267 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9PE7

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of Atirmociclib (PF-07220060): A Potent and Selective CDK4 Inhibitor.

Gallego, G.M.Palmer, C.Orr, S.Bernier, L.Chen, P.Cho-Schultz, S.Deal, J.G.Dress, K.Edwards, M.Jalaie, M.Johnson, E.Kania, R.Kath, J.C.Lafontaine, J.Ninkovic, S.Sach, N.Shen, H.Anders, L.Boras, B.Cao, F.Cianfrogna, J.A.Cox, L.Marroquin, L.Pascual, B.Petroski, M.Quinlan, C.Sacaan, A.Wei, N.Nair, S.K.

(2025) J Med Chem 68: 26085-26098

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c02137
  • Primary Citation Related Structures: 
    9PE7, 9PE8, 9PE9

  • PubMed Abstract: 

    Inhibitors of cyclin-dependent kinases 4 and 6 have been shown to be clinically effective for the treatment of hormone receptor-positive (HR+), human epidermal growth factor receptor 2-negative (HER2-) advanced, or metastatic breast cancer. These agents, however, often show neutropenia, likely due to the role of CDK6 in hematopoiesis. Herein described is the discovery of a series of aminopyrimidine-based selective CDK4 inhibitors. Central to our strategy were efficiency-based optimization (LipE and LipMetE), structure-based drug design, and molecular dynamics simulation. The culmination of these efforts resulted in the discovery of PF-07220060 (atirmociclib), which possessed high potency and levels of selectivity for CDK4 over CDK6 that translated to minimal impact on neutrophils while driving efficacy in a mouse ZR75-1 xenograft model.


  • Organizational Affiliation
    • Oncology Medicinal Chemistry, Pfizer Worldwide Research and Development, La Jolla, San Diego, California 92121, United States.

Macromolecule Content 

  • Total Structure Weight: 35.5 kDa 
  • Atom Count: 2,255 
  • Modeled Residue Count: 262 
  • Deposited Residue Count: 307 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 6307Homo sapiensMutation(s): 4 
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CIF
(Subject of Investigation/LOI)

Query on A1CIF



Download:Ideal Coordinates CCD File
B [auth A](3R,4R)-4-({(4M)-5-fluoro-4-[4-fluoro-2-methyl-1-(propan-2-yl)-1H-1,3-benzimidazol-6-yl]pyrimidin-2-yl}amino)-1-(methanesulfonyl)piperidin-3-ol
C21 H26 F2 N6 O3 S
UKVZKVRVVNTCMR-SJLPKXTDSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.267 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.44α = 90
b = 101.44β = 90
c = 59.8γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
STARANISOdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release
  • Version 1.1: 2025-12-31
    Changes: Database references