3NUP | pdb_00003nup

CDK6 (monomeric) in complex with inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.264 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.230 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3NUClick on this verticalbar to view details

This is version 1.4 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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3NU
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
YVKZWLZGQQCODL-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.264 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.230 (DCC) 
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
CNSrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
d*TREKdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3NUClick on this verticalbar to view details

View more in-depth experimental data
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