3ULI

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

• PDB DOI: https://doi.org/10.2210/pdb3ULI/pdb

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


• Deposited: 2011-11-10 Released: 2013-08-14 
• Deposition Author(s): Larsen, N.A., Tucker, J.A., Wang, T.

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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 

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

• PubMed: 22305584 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

Department of Cancer Chemistry, Oncology Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.45 kDa 
• Atom Count: 2,456 
• Modelled Residue Count: 286 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2	A	298	Homo sapiens	Mutation(s): 0  Gene Names: CDK2, CDKN2 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 GTEx:  ENSG00000123374

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1N3	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

Binding Affinity Annotations
ID	Source	Binding Affinity
1N3	PDBBind:  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 = 53.304	α = 90
b = 71.352	β = 90
c = 71.914	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-14 
Deposition Author(s): Larsen, N.A., Tucker, J.A., Wang, T.

Revision History  

• Version 1.0: 2013-08-14
  Type: Initial release
  
• Version 1.1: 2013-09-04
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations