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

Experimental Data Snapshot

  • Resolution: 2.31 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYCLIN-DEPENDENT KINASE 6307Homo sapiensMutation(s): 0 
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 4AU

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

Experimental Data

  • Resolution: 2.31 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • 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
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

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