3IG7

Novel CDK-5 inhibitors - crystal structure of inhibitor EFP with CDK-2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Potent and cellularly active 4-aminoimidazole inhibitors of cyclin-dependent kinase 5/p25 for the treatment of Alzheimer's disease.

Helal, C.J., Kang, Z., Lucas, J.C., Gant, T., Ahlijanian, M.K., Schachter, J.B., Richter, K.E., Cook, J.M., Menniti, F.S., Kelly, K., Mente, S., Pandit, J., Hosea, N.

(2009) Bioorg Med Chem Lett 19: 5703-5707

  • DOI: 10.1016/j.bmcl.2009.08.019
  • Primary Citation of Related Structures:  
    3IGG, 3IG7

  • PubMed Abstract: 

    • Utilizing structure-based drug design, a 4-aminoimidazole heterocyclic core was synthesized as a replacement for a 2-aminothiazole due to potential metabolically mediated toxicity. The synthetic route utilized allowed for ready synthesis of 1-substituted-4-aminoimidazoles ...

    Utilizing structure-based drug design, a 4-aminoimidazole heterocyclic core was synthesized as a replacement for a 2-aminothiazole due to potential metabolically mediated toxicity. The synthetic route utilized allowed for ready synthesis of 1-substituted-4-aminoimidazoles. SAR exploration resulted in the identification of a novel cis-substituted cyclobutyl group that gave improved enzyme and cellular potency against cdk5/p25 with up to 30-fold selectivity over cdk2/cyclin E.

    Organizational Affiliation: 

    Neuroscience Medicinal Chemistry, Pfizer Global Research and Development, Eastern Point Road, Groton, CT 06340, USA. chris.j.helal@pfizer.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division protein kinase 2A299Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EFP (Subject of Investigation/LOI)
Query on EFP
Download Ideal Coordinates CCD File 
 B [auth A]N-{1-[cis-3-(acetylamino)cyclobutyl]-1H-imidazol-4-yl}-2-(4-methoxyphenyl)acetamide
C18 H22 N4 O3
PUVVKKBHOWNLRX-GASCZTMLSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EFP PDBBind:  3IG7 IC50: 63 (nM) from 1 assay(s)
Binding MOAD:  3IG7 IC50: 9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.343α = 90
b = 70.994β = 90
c = 71.811γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment  


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Entry History 

Deposition Data

  • Deposited Date: 2009-07-27 
  • Released Date: 2009-09-08 
    • Deposition Author(s): Pandit, J.

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance