1YKR

Crystal structure of cdk2 with an aminoimidazo pyridine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1016/j.bmcl.2005.01.052
  • Primary Citation of Related Structures:  
    1YKR

  • 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 identif ...

    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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division protein kinase 2A298Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (UniProt)
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS  P24941
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
628
Query on 628

Download CCD File 
A
4-{[6-(2,6-DICHLOROBENZOYL)IMIDAZO[1,2-A]PYRIDIN-2-YL]AMINO}BENZENESULFONAMIDE
C20 H14 Cl2 N4 O3 S
UQAWGIKJINAKIZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
628IC50:  560   nM  Binding MOAD
628IC50 :  560   nM  PDBBind
628IC50:  560   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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