7SJ3 | pdb_00007sj3

Structure of CDK4-Cyclin D3 bound to abemaciclib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 
    0.234 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of active CDK4-cyclin D and mechanistic basis for abemaciclib efficacy.

Gharbi, S.I.Pelletier, L.A.Espada, A.Gutierrez, J.Sanfeliciano, S.M.G.Rauch, C.T.Ganado, M.P.Baquero, C.Zapatero, E.Zhang, A.Benach, J.Russell, A.M.Cano, L.Gomez, S.Broughton, H.Pulliam, N.Perez, C.M.Torres, R.Debets, M.F.de Dios, A.Puig, O.Hilgers, M.T.Lallena, M.J.

(2022) NPJ Breast Cancer 8: 126-126

  • DOI: https://doi.org/10.1038/s41523-022-00494-y
  • Primary Citation of Related Structures:  
    7SJ3

  • PubMed Abstract: 

    Despite the biological and therapeutic relevance of CDK4/6 for the treatment of HR+, HER2- advanced breast cancer, the detailed mode of action of CDK4/6 inhibitors is not completely understood. Of particular interest, phosphorylation of CDK4 at T172 (pT172) is critical for generating the active conformation, yet no such crystal structure has been reported to date. We describe here the x-ray structure of active CDK4-cyclin D3 bound to the CDK4/6 inhibitor abemaciclib and discuss the key aspects of the catalytically-competent complex. Furthermore, the effect of CDK4/6 inhibitors on CDK4 T172 phosphorylation has not been explored, despite its role as a potential biomarker of CDK4/6 inhibitor response. We show mechanistically that CDK4/6i stabilize primed (pT172) CDK4-cyclin D complex and selectively displace p21 in responsive tumor cells. Stabilization of active CDK4-cyclin D1 complex can lead to pathway reactivation following alternate dosing regimen. Consequently, sustained binding of abemaciclib to CDK4 leads to potent cell cycle inhibition in breast cancer cell lines and prevents rebound activation of downstream signaling. Overall, our study provides key insights demonstrating that prolonged treatment with CDK4/6 inhibitors and composition of the CDK4/6-cyclin D complex are both critical determinants of abemaciclib efficacy, with implications for this class of anticancer therapy.


  • Organizational Affiliation

    Discovery Chemistry Research & Technology, Eli Lilly and Company, Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 4311Homo sapiensMutation(s): 1 
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
G1/S-specific cyclin-D3259Homo sapiensMutation(s): 0 
Gene Names: CCND3
UniProt & NIH Common Fund Data Resources
Find proteins for P30281 (Homo sapiens)
Explore P30281 
Go to UniProtKB:  P30281
PHAROS:  P30281
GTEx:  ENSG00000112576 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30281
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6ZV (Subject of Investigation/LOI)
Query on 6ZV

Download Ideal Coordinates CCD File 
C [auth A]N-{5-[(4-ethylpiperazin-1-yl)methyl]pyridin-2-yl}-5-fluoro-4-[4-fluoro-2-methyl-1-(propan-2-yl)-1H-benzimidazol-6-yl]py rimidin-2-amine
C27 H32 F2 N8
UZWDCWONPYILKI-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
6ZV BindingDB:  7SJ3 Ki: min: 2, max: 8.2 (nM) from 2 assay(s)
IC50: min: 0.26, max: 1700 (nM) from 18 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free:  0.234 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.654α = 90
b = 117.654β = 90
c = 170.278γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited StatesNA

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-02
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary
  • Version 1.3: 2025-06-11
    Changes: Database references