CDK6 (monomeric) in complex with inhibitor

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.238 

Starting Model: experimental
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4-(Pyrazol-4-yl)-pyrimidines as selective inhibitors of cyclin-dependent kinase 4/6.

Cho, Y.S.Borland, M.Brain, C.Chen, C.H.Cheng, H.Chopra, R.Chung, K.Groarke, J.He, G.Hou, Y.Kim, S.Kovats, S.Lu, Y.O'Reilly, M.Shen, J.Smith, T.Trakshel, G.Vogtle, M.Xu, M.Xu, M.Sung, M.J.

(2010) J Med Chem 53: 7938-7957

  • DOI: https://doi.org/10.1021/jm100571n
  • Primary Citation of Related Structures:  
    3NUP, 3NUX

  • PubMed Abstract: 

    Identification and structure-guided optimization of a series of 4-(pyrazol-4-yl)-pyrimidines as selective CDK4/6 inhibitors is reported herein. Several potency and selectivity determinants were established based on the X-ray crystallographic analysis of representative compounds bound to monomeric CDK6. Significant selectivity for CDK4/6 over CDK1 and CDK2 was demonstrated with several compounds in both enzymatic and cellular assays.

  • Organizational Affiliation

    Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA. youngshin.cho@novartis

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division protein kinase 6307Homo sapiensMutation(s): 0 
Gene Names: CDK6
UniProt & NIH Common Fund Data Resources
Find proteins for Q00534 (Homo sapiens)
Explore Q00534 
Go to UniProtKB:  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
Query on 3NU

Download Ideal Coordinates CCD File 
B [auth A]4-[3-(1-methylethyl)-1H-pyrazol-4-yl]-N-(1-methylpiperidin-4-yl)pyrimidin-2-amine
C16 H24 N6
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.238 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.778α = 90
b = 101.778β = 90
c = 59.296γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
PDB_EXTRACTdata extraction
StructureStudiodata collection
d*TREKdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2010-12-22 
  • Deposition Author(s): Chopra, R.

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description