4AUA

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

• PDB DOI: https://doi.org/10.2210/pdb4AUA/pdb

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


• Deposited: 2012-05-15 Released: 2013-02-06 
• Deposition Author(s): Cho, Y.S., Angove, H., Brain, C., Chen, C.H.T., Cheng, R., Chopra, R., Chung, K., Congreve, M., Dagostin, C., Davis, D., Feltell, R., Giraldes, J., Hiscock, S., Kim, S., Kovats, S., Lagu, B., Lewry, K., Loo, A., Lu, Y., Luzzio, M., Maniara, W., Mcmenamin, R., Mortenson, P., Benning, R., O'Reilly, M., Rees, D., Shen, J., Smith, T., Wang, Y., Williams, G., Woolford, A., Wrona, W., Xu, M., Yang, F., Howard, S.

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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 

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

• PubMed: 24900493 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.23 kDa 
• Atom Count: 2,150 
• Modelled Residue Count: 256 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLIN-DEPENDENT KINASE 6	A	307	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4AU	B [auth A]	1H-benzimidazol-2-yl(1H-pyrrol-2-yl)methanone C12 H9 N3 O WKGKIJSPPFRZEQ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4AU	PDBBind:  4AUA	IC50: 7200 (nM) from 1 assay(s)
	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 
• R-Value Work: 0.207 
• R-Value Observed: 0.210 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.734	α = 90
b = 100.734	β = 90
c = 60.3	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-06 
Deposition Author(s): Cho, Y.S., Angove, H., Brain, C., Chen, C.H.T., Cheng, R., Chopra, R., Chung, K., Congreve, M., Dagostin, C., Davis, D., Feltell, R., Giraldes, J., Hiscock, S., Kim, S., Kovats, S., Lagu, B., Lewry, K., Loo, A., Lu, Y., Luzzio, M., Maniara, W., Mcmenamin, R., Mortenson, P., Benning, R., O'Reilly, M., Rees, D., Shen, J., Smith, T., Wang, Y., Williams, G., Woolford, A., Wrona, W., Xu, M., Yang, F., Howard, S.

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
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other