3ULI

Human Cyclin Dependent Kinase 2 (CDK2) bound to azabenzimidazole derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.238 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of azabenzimidazole derivatives as potent, selective inhibitors of TBK1/IKK epsilon kinases.

Wang, T.Block, M.A.Cowen, S.Davies, A.M.Devereaux, E.Gingipalli, L.Johannes, J.Larsen, N.A.Su, Q.Tucker, J.A.Whitston, D.Wu, J.Zhang, H.J.Zinda, M.Chuaqui, C.

(2012) Bioorg Med Chem Lett 22: 2063-2069

  • DOI: 10.1016/j.bmcl.2012.01.018
  • Primary Citation of Related Structures:  
    3ULI

  • PubMed Abstract: 
  • The design, synthesis and biological evaluation of a series of azabenzimidazole derivatives as TBK1/IKKε kinase inhibitors are described. Starting from a lead compound 1a, iterative design and SAR exploitation of the scaffold led to analogues with nM enzyme potencies against TBK1/IKKε ...

    The design, synthesis and biological evaluation of a series of azabenzimidazole derivatives as TBK1/IKKε kinase inhibitors are described. Starting from a lead compound 1a, iterative design and SAR exploitation of the scaffold led to analogues with nM enzyme potencies against TBK1/IKKε. These compounds also exhibited excellent cellular activity against TBK1. Further structure-based design to improve selectivity over CDK2 and Aurora B resulted in compounds such as 5b-e. These probe compounds will facilitate study of the complex cancer biology of TBK1 and IKKε.


    Organizational Affiliation

    Department of Cancer Chemistry, Oncology Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA. tao.wang@astrazeneca.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase 2A298Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
PHAROS:  P24941
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1N3 (Subject of Investigation/LOI)
Query on 1N3

Download Ideal Coordinates CCD File 
B [auth A]1-(aminomethyl)-N-(3-{[6-bromo-2-(4-methoxyphenyl)-3H-imidazo[4,5-b]pyridin-7-yl]amino}propyl)cyclopropanecarboxamide
C21 H25 Br N6 O2
XUELBKVSGYWSKD-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1N3 PDBBind:  3ULI IC50: 70 (nM) from 1 assay(s)
Binding MOAD:  3ULI IC50: 70 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.304α = 90
b = 71.352β = 90
c = 71.914γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-14
    Type: Initial release
  • Version 1.1: 2013-09-04
    Changes: Database references