CDK6 in complex with Cpd13 (R)-5-fluoro-4-(4-methyl-5,6,7,8-tetrahydro-4H-pyrazolo[1,5-a]azepin-3-yl)-N-(5-(4-methylpiperazin-1-yl)pyridin-2-yl)pyrimidin-2-amine

Experimental Data Snapshot

  • Resolution: 2.71 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

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Design of a brain-penetrant CDK4/6 inhibitor for glioblastoma.

Bronner, S.M.Merrick, K.A.Murray, J.Salphati, L.Moffat, J.G.Pang, J.Sneeringer, C.J.Dompe, N.Cyr, P.Purkey, H.Boenig, G.L.Li, J.Kolesnikov, A.Larouche-Gauthier, R.Lai, K.W.Shen, X.Aubert-Nicol, S.Chen, Y.C.Cheong, J.Crawford, J.J.Hafner, M.Haghshenas, P.Jakalian, A.Leclerc, J.P.Lim, N.K.O'Brien, T.Plise, E.G.Shalan, H.Sturino, C.Wai, J.Xiao, Y.Yin, J.Zhao, L.Gould, S.Olivero, A.Heffron, T.P.

(2019) Bioorg Med Chem Lett 29: 2294-2301

  • DOI: https://doi.org/10.1016/j.bmcl.2019.06.021
  • Primary Citation of Related Structures:  
    6OQI, 6OQL, 6OQO

  • PubMed Abstract: 

    CDK4 and CDK6 are kinases with similar sequences that regulate cell cycle progression and are validated targets in the treatment of cancer. Glioblastoma is characterized by a high frequency of CDKN2A/CCND2/CDK4/CDK6 pathway dysregulation, making dual inhibition of CDK4 and CDK6 an attractive therapeutic approach for this disease. Abemaciclib, ribociclib, and palbociclib are approved CDK4/6 inhibitors for the treatment of HR+/HER2- breast cancer, but these drugs are not expected to show strong activity in brain tumors due to poor blood brain barrier penetration. Herein, we report the identification of a brain-penetrant CDK4/6 inhibitor derived from a literature molecule with low molecular weight and topological polar surface area (MW = 285 and TPSA = 66 Å 2 ), but lacking the CDK2/1 selectivity profile due to the absence of a basic amine. Removal of a hydrogen bond donor via cyclization of the pyrazole allowed for the introduction of basic and semi-basic amines, while maintaining in many cases efflux ratios reasonable for a CNS program. Ultimately, a basic spiroazetidine (cpK a  = 8.8) was identified that afforded acceptable selectivity over anti-target CDK1 while maintaining brain-penetration in vivo (mouse K p,uu  = 0.20-0.59). To probe the potency and selectivity, our lead compound was evaluated in a panel of glioblastoma cell lines. Potency comparable to abemaciclib was observed in Rb-wild type lines U87MG, DBTRG-05MG, A172, and T98G, while Rb-deficient cell lines SF539 and M059J exhibited a lack of sensitivity.

  • Organizational Affiliation

    Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States. Electronic address: sbronner@mazetx.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 6291Homo sapiensMutation(s): 0 
Gene Names: CDK6CDKN6
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N1A (Subject of Investigation/LOI)
Query on N1A

Download Ideal Coordinates CCD File 
B [auth A]5-fluoro-N-[5-(4-methylpiperazin-1-yl)pyridin-2-yl]-4-[(4R)-4-methyl-5,6,7,8-tetrahydro-4H-pyrazolo[1,5-a]azepin-3-yl]pyrimidin-2-amine
C23 H29 F N8
Experimental Data & Validation

Experimental Data

  • Resolution: 2.71 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.668α = 90
b = 101.668β = 90
c = 60.113γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2020-07-29 
  • Deposition Author(s): Murray, J.M.

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2021-08-11
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Refinement description