9GOP | pdb_00009gop

Crystal structure of CDK2-cyclin E1 bound by compound 30


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 
    0.271 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of AZD8421: A Potent CDK2 Inhibitor with Selectivity Against Other CDK Family Members and the Human Kinome.

Ghosh, A.Ahmed, A.Amoiradaki, K.Balazs, A.Y.S.Barlaam, B.Bodnarchuk, M.S.Collie, G.W.Dale, I.L.Denz, C.R.Drew, L.Edmondson, S.D.Fan, J.Fawell, S.Goldberg, F.W.Gopalsamy, A.Grondine, M.Guo, G.Hande, S.M.Hatoum-Mokdad, H.Hird, A.W.Howells, R.Hao-Ru Hsu, J.Hudson, J.Jackson, A.Lamb, M.L.Lamont, G.M.Lamont, S.Lichtor, P.A.McWilliams, L.Milne, D.Mlynarski, S.N.Narasimhan, P.Peters, M.F.Pflug, A.Pollard, H.K.Qin, M.Reimer, C.Robbins, K.J.Robinson, J.Sha, L.She, H.Sheppeck 2nd, J.E.Singh, B.Song, K.Su, Q.Telmesani, R.Throner, S.Vasalou, C.Wang, L.Wang, Y.Wilson, D.M.Winlow, P.Yang, W.Yao, T.Zhang, Y.Zhang, Z.Zindel, D.Johannes, J.W.

(2025) J Med Chem 68: 18164-18177

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01478
  • Primary Citation of Related Structures:  
    9GNO, 9GOP, 9GP3

  • PubMed Abstract: 

    Targeting CDK2 with first generation CDK2 inhibitors suffered from a reduced therapeutic index likely due to toxicity stemming from lack of selectivity against the CDK family and other kinases. Recently, CDK2 has been identified as a mediator of resistance to CDK4/6 inhibitors in the context of high levels of cyclin E expression. Discovery of highly selective CDK2 inhibitors may minimize off-target effects, reduce toxicity observed with first generation CDK2 inhibitors, and allow precise targeting of aberrant cell cycle progression and resistance mechanisms mediated by high cyclin E/CDK2 activity. To this end, we report the discovery of AZD8421, a potent and highly selective CDK2 inhibitor, which exhibits superior selectivity for CDK2 over CDK1, other CDK family members, and the broader human kinome. AZD8421 demonstrates favorable pharmacokinetic properties, including excellent solubility and robust in vitro stability. Demonstrated efficacy in an ovarian cancer patient-derived xenograft model further supports its potential as a therapeutic agent.


  • Organizational Affiliation
    • Chemistry, Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 2298Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
PHAROS:  P24941
GTEx:  ENSG00000123374 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24941
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-E1285Homo sapiensMutation(s): 0 
Gene Names: CCNE1CCNE
UniProt & NIH Common Fund Data Resources
Find proteins for P24864 (Homo sapiens)
Explore P24864 
Go to UniProtKB:  P24864
PHAROS:  P24864
GTEx:  ENSG00000105173 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24864
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IOI (Subject of Investigation/LOI)
Query on A1IOI

Download Ideal Coordinates CCD File 
C [auth A]2-[(2~{S})-1-[9-ethyl-6-[(2-methyl-5-methylsulfonyl-pyrazol-3-yl)amino]purin-2-yl]-4,4-bis(fluoranyl)pyrrolidin-2-yl]propan-2-ol
C19 H26 F2 N8 O3 S
BBESOAAPFWJUGQ-NSHDSACASA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free:  0.271 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.291α = 90
b = 102.291β = 90
c = 153.071γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-09-10 
  • Deposition Author(s): Collie, G.W.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release
  • Version 1.1: 2025-09-17
    Changes: Database references
  • Version 1.2: 2025-09-24
    Changes: Database references