3IG7

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

• PDB DOI: https://doi.org/10.2210/pdb3IG7/pdb

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


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

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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 

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

• PubMed: 19700321 
• DOI: https://doi.org/10.1016/j.bmcl.2009.08.019
• Primary Citation of Related Structures:  
  3IG7, 3IGG


• 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. 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.

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Organizational Affiliation: 

Neuroscience Medicinal Chemistry, Pfizer Global Research and Development, Eastern Point Road, Groton, CT 06340, 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: 34.34 kDa 
• Atom Count: 2,334 
• Modelled Residue Count: 279 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein kinase 2	A	299	Homo sapiens	Mutation(s): 0  Gene Names: CDK2 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
EFP	B [auth A]	N-{1-[cis-3-(acetylamino)cyclobutyl]-1H-imidazol-4-yl}-2-(4-methoxyphenyl)acetamide C18 H22 N4 O3 PUVVKKBHOWNLRX-GASCZTMLSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EFP	PDBBind:  3IG7	IC50: 63 (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 = 53.343	α = 90
b = 70.994	β = 90
c = 71.811	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2009-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary