Crystal structure of cdk2 with an aminoimidazo pyridine inhibitor

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.260 

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This is version 1.3 of the entry. See complete history


Structure-based design of a new class of highly selective aminoimidazo[1,2-a]pyridine-based inhibitors of cyclin dependent kinases

Hamdouchi, C.Zhong, B.Mendoza, J.Collins, E.Jaramillo, C.De Diego, J.E.Robertson, D.Spencer, C.D.Anderson, B.D.Watkins, S.A.Zhang, F.Brooks, H.B.

(2005) Bioorg Med Chem Lett 15: 1943-1947

  • DOI: https://doi.org/10.1016/j.bmcl.2005.01.052
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Structure-based design approach was successfully used to guide the evolution of imidazopyridine scaffold yielding new structural class of highly selective inhibitors of cyclin dependent kinases that were able to form a new interaction with an identified residue of the protein, Lys89. Compounds from this series have shown no detectable effect when tested against a representative set of other serine/threonine kinases such as GSK3beta, CAMKII, PKA, PKC-alpha,beta,epsilon,gamma. Compound 2i inhibits proliferation in HCT 116 cells in tissue culture. Synthesis, co-crystal structure of CDK2 in complex with compound 2i, and preliminary SAR study are disclosed.

  • Organizational Affiliation

    Lilly Research Laboratories, A Division of Eli Lilly and Company, Lilly Corporate Center, DC: 0540, Indianapolis, IN 46285, United States. hamdouchi_chafiq@lilly.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division protein kinase 2298Homo sapiensMutation(s): 0 
Gene Names: CDK2
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
PHAROS:  P24941
GTEx:  ENSG00000123374 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24941
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 628

Download Ideal Coordinates CCD File 
C20 H14 Cl2 N4 O3 S
Binding Affinity Annotations 
IDSourceBinding Affinity
628 BindingDB:  1YKR IC50: 560 (nM) from 1 assay(s)
Binding MOAD:  1YKR IC50: 560 (nM) from 1 assay(s)
PDBBind:  1YKR IC50: 560 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.260 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.25α = 90
b = 71.393β = 90
c = 71.418γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description