4AUA

Liganded X-ray crystal structure of cyclin dependent kinase 6 (CDK6)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 
    0.277 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

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 4AUClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Fragment-Based Discovery of 7-Azabenzimidazoles as Potent, Highly Selective, and Orally Active CDK4/6 Inhibitors.

Cho, Y.S.Angove, H.Brain, C.Chen, C.H.Cheng, H.Cheng, R.Chopra, R.Chung, K.Congreve, M.Dagostin, C.Davis, D.J.Feltell, R.Giraldes, J.Hiscock, S.D.Kim, S.Kovats, S.Lagu, B.Lewry, K.Loo, A.Lu, Y.Luzzio, M.Maniara, W.McMenamin, R.Mortenson, P.N.Benning, R.O'Reilly, M.Rees, D.C.Shen, J.Smith, T.Wang, Y.Williams, G.Woolford, A.J.Wrona, W.Xu, M.Yang, F.Howard, S.

(2012) ACS Med Chem Lett 3: 445-449

  • DOI: https://doi.org/10.1021/ml200241a
  • Primary Citation of Related Structures:  
    4AUA, 4EZ5

  • PubMed Abstract: 

    Herein, we describe the discovery of potent and highly selective inhibitors of both CDK4 and CDK6 via structure-guided optimization of a fragment-based screening hit. CDK6 X-ray crystallography and pharmacokinetic data steered efforts in identifying compound 6, which showed >1000-fold selectivity for CDK4 over CDKs 1 and 2 in an enzymatic assay. Furthermore, 6 demonstrated in vivo inhibition of pRb-phosphorylation and oral efficacy in a Jeko-1 mouse xenograft model.


  • Organizational Affiliation

    Novartis Institutes for Biomedical Research , 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYCLIN-DEPENDENT KINASE 6307Homo sapiensMutation(s): 0 
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
4AU
Query on 4AU

Download Ideal Coordinates CCD File 
B [auth A]1H-benzimidazol-2-yl(1H-pyrrol-2-yl)methanone
C12 H9 N3 O
WKGKIJSPPFRZEQ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
4AU BindingDB:  4AUA IC50: 7200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free:  0.277 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.734α = 90
b = 100.734β = 90
c = 60.3γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

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 4AUClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-06
    Type: Initial release
  • Version 1.1: 2014-06-18
    Changes: Database references
  • Version 1.2: 2018-02-07
    Changes: Database references, Structure summary
  • Version 1.3: 2019-04-03
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other