5EKV

Co-crystal structure of eIF4E with nucleotide mimetic inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.61 Å
  • R-Value Free: 0.342 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.270 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Design of nucleotide-mimetic and non-nucleotide inhibitors of the translation initiation factor eIF4E: Synthesis, structural and functional characterisation.

Soukarieh, F.Nowicki, M.W.Bastide, A.Poyry, T.Jones, C.Dudek, K.Patwardhan, G.Meullenet, F.Oldham, N.J.Walkinshaw, M.D.Willis, A.E.Fischer, P.M.

(2016) Eur J Med Chem 124: 200-217

  • DOI: 10.1016/j.ejmech.2016.08.047
  • Primary Citation of Related Structures:  
    5EI3, 5EHC, 5EIR, 5EKV

  • PubMed Abstract: 
  • Eukaryotic translation initiation factor 4E (eIF4E) is considered as the corner stone in the cap-dependent translation initiation machinery. Its role is to recruit mRNA to the ribosome through recognition of the 5'-terminal mRNA cap structure (m 7 GpppN, where G is guanosine, N is any nucleotide) ...

    Eukaryotic translation initiation factor 4E (eIF4E) is considered as the corner stone in the cap-dependent translation initiation machinery. Its role is to recruit mRNA to the ribosome through recognition of the 5'-terminal mRNA cap structure (m 7 GpppN, where G is guanosine, N is any nucleotide). eIF4E is implicated in cell transformation, tumourigenesis, and angiogenesis by facilitating translation of oncogenic mRNAs; it is thus regarded as an attractive anticancer drug target. We have used two approaches to design cap-binding inhibitors of eIF4E by modifying the N 7 -substituent of m 7 GMP and replacing the phosphate group with isosteres such as squaramides, sulfonamides, and tetrazoles, as well as by structure-based virtual screening aimed at identifying non-nucleotide cap-binding antagonists. Phosphomimetic nucleotide derivatives and highly ranking virtual hits were evaluated in a series of in vitro and cell-based assays to identify the first non-nucleotide eIF4E cap-binding inhibitor with activities in cell-based assays, N-[(5,6-dihydro-6-oxo-1,3-dioxolo[4,5-g]quinolin-7-yl)methyl]-N'-(2-methyl-propyl)-N-(phenyl-methyl)thiourea (14), including down-regulation of oncogenic proteins and suppression of RNA incorporation into polysomes. Although we did not observe cellular activity with any of our modified m 7 GMP phosphate isostere compounds, we obtained X-ray crystallography structures of three such compounds in complex with eIF4E, 5'-deoxy-5'-(1,2-dioxo-3-hydroxycyclobut-3-en-4-yl)amino-N 7 -methyl-guanosine (4a), N 7 -3-chlorobenzyl-5'-deoxy-5'-(1,2-dioxo-3-hydroxy-cyclobut-3-en-4-yl)amino-guanosine (4f), and N 7 -benzyl-5'-deoxy-5'-(trifluoromethyl-sulfamoyl)guanosine (7a). Collectively, the data we present on structure-based design of eIF4E cap-binding inhibitors should facilitate the optimisation of such compounds as potential anticancer agents.


    Organizational Affiliation

    School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK. Electronic address: peter.fischer@nottingham.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 4E AC217Homo sapiensMutation(s): 0 
Gene Names: EIF4EEIF4EL1EIF4F
Find proteins for P06730 (Homo sapiens)
Explore P06730 
Go to UniProtKB:  P06730
NIH Common Fund Data Resources
PHAROS:  P06730
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 4E-binding protein 1 BD14Homo sapiensMutation(s): 0 
Gene Names: EIF4EBP1
Find proteins for Q13541 (Homo sapiens)
Explore Q13541 
Go to UniProtKB:  Q13541
NIH Common Fund Data Resources
PHAROS:  Q13541
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5PQ
Query on 5PQ

Download Ideal Coordinates CCD File 
A, C
3-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-4-oxidanyl-cyclobut-3-ene-1,2-dione
C15 H17 N6 O7
WRZJZJPEHQGNLE-CZCBHZRKSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.61 Å
  • R-Value Free: 0.342 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.270 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.48α = 90
b = 100.78β = 90
c = 136.46γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2016-09-14
    Changes: Database references