4DT6

Co-crystal structure of eIF4E with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1021/jm300037x
  • Primary Citation of Related Structures:  

  • 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 displa ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 4E
A
240Homo sapiensMutation(s): 0 
Gene Names: EIF4E (EIF4EL1, EIF4F)
Find proteins for P06730 (Homo sapiens)
Go to Gene View: EIF4E
Go to UniProtKB:  P06730
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
6LI
Query on 6LI

Download SDF File 
Download CCD File 
A
7-[2-(4-chlorophenoxy)ethyl]guanosine 5'-(dihydrogen phosphate)
C18 H22 Cl N5 O9 P
QWFXGVANFMDSMH-LSCFUAHRSA-O
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6LIIC50: 59 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.224α = 90.00
b = 61.073β = 90.00
c = 122.439γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
BOSdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-11
    Type: Initial release
  • Version 1.1: 2012-05-02
    Type: Database references
  • Version 1.2: 2012-06-27
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description