4DT6

Co-crystal structure of eIF4E with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure-Guided Design, Synthesis, and Evaluation of Guanine-Derived Inhibitors of the eIF4E mRNA-Cap Interaction.

Chen, X.Kopecky, D.J.Mihalic, J.Jeffries, S.Min, X.Heath, J.Deignan, J.Lai, S.Fu, Z.Guimaraes, C.Shen, S.Li, S.Johnstone, S.Thibault, S.Xu, H.Cardozo, M.Shen, W.Walker, N.Kayser, F.Wang, Z.

(2012) J Med Chem 55: 3837-3851

  • DOI: https://doi.org/10.1021/jm300037x
  • Primary Citation of Related Structures:  
    4DT6, 4DUM

  • PubMed Abstract: 

    The eukaryotic initiation factor 4E (eIF4E) plays a central role in the initiation of gene translation and subsequent protein synthesis by binding the 5' terminal mRNA cap structure. We designed and synthesized a series of novel compounds that display potent binding affinity against eIF4E despite their lack of a ribose moiety, phosphate, and positive charge as present in m7-GMP. The biochemical activity of compound 33 is 95 nM for eIF4E in an SPA binding assay. More importantly, the compound has an IC(50) of 2.5 μM for inhibiting cap-dependent mRNA translation in a rabbit reticular cell extract assay (RRL-IVT). This series of potent, truncated analogues could serve as a promising new starting point toward the design of neutral eIF4E inhibitors with physicochemical properties suitable for cellular activity assessment.


  • Organizational Affiliation

    Department of Chemistry Research & Discovery, Amgen Inc., 1120 Veterans Boulevard, South San Francisco, California 94080, USA. xiaoqic@amgen.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 4E240Homo sapiensMutation(s): 0 
Gene Names: EIF4EEIF4EL1EIF4F
UniProt & NIH Common Fund Data Resources
Find proteins for P06730 (Homo sapiens)
Explore P06730 
Go to UniProtKB:  P06730
PHAROS:  P06730
GTEx:  ENSG00000151247 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06730
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.224α = 90
b = 61.073β = 90
c = 122.439γ = 90
Software Package:
Software NamePurpose
BOSdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-11
    Type: Initial release
  • Version 1.1: 2012-05-02
    Changes: Database references
  • Version 1.2: 2012-06-27
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Derived calculations