3NUX

CDK6 (monomeric) in complex with inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.243 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

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


Macromolecules
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
EC: 2.7.11.22
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3NV
Query on 3NV
Download Ideal Coordinates CCD File 
B [auth A]4-[5-chloro-3-(1-methylethyl)-1H-pyrazol-4-yl]-N-(5-piperazin-1-ylpyridin-2-yl)pyrimidin-2-amine
C19 H23 Cl N8
ZGJLAVYYTJNBMN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.243 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.96α = 90
b = 101.96β = 90
c = 59.66γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
d*TREKdata reduction
MOLREPphasing
CNXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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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