3NUP

CDK6 (monomeric) in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3NUP/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2010-07-07 Released: 2010-12-22 
• Deposition Author(s): Chopra, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.264 
• R-Value Work: 0.238 

Starting Model: experimental

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

• PubMed: 21038853 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.32 kDa 
• Atom Count: 2,067 
• Modelled Residue Count: 252 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein kinase 6	A	307	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3NU	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 
• R-Value Work: 0.238 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.778	α = 90
b = 101.778	β = 90
c = 59.296	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
d*TREK	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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