9PE9 | pdb_00009pe9

GSK3beta in complex with compound 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 
    0.247 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9PE9

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: 82.73 kDa 
  • Atom Count: 5,775 
  • Modeled Residue Count: 664 
  • Deposited Residue Count: 718 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycogen synthase kinase-3 beta
A, B
359Homo sapiensMutation(s): 0 
Gene Names: GSK3B
EC: 2.7.11.26 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P49841 (Homo sapiens)
Explore P49841 
Go to UniProtKB:  P49841
PHAROS:  P49841
GTEx:  ENSG00000082701 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49841
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
C [auth A],
D [auth B]
(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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A, B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free:  0.247 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.63α = 90
b = 109.25β = 100.99
c = 67.65γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
autoBUSTERphasing

Structure Validation

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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