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 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1021/ml200241a
  • Primary Citation of Related Structures:  
    4EZ5, 4AUA

  • 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 ...

    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

    Astex Pharmaceuticals Inc. , 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLIN-DEPENDENT KINASE 6A307Homo sapiensMutation(s): 0 
Gene Names: CDK6CDKN6
EC: 2.7.11.22
Find proteins for Q00534 (Homo sapiens)
Explore Q00534 
Go to UniProtKB:  Q00534
NIH Common Fund Data Resources
PHAROS  Q00534
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4AU
Query on 4AU

Download CCD File 
A
1H-benzimidazol-2-yl(1H-pyrrol-2-yl)methanone
C12 H9 N3 O
WKGKIJSPPFRZEQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4AUIC50:  7200   nM  BindingDB
4AUIC50 :  7200   nM  PDBBind
4AUIC50:  7200   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • 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