8SX4

Crystal Structure of eIF4e in complex with Compound 7n


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Design of Cell-Permeable Inhibitors of Eukaryotic Translation Initiation Factor 4E (eIF4E) for Inhibiting Aberrant Cap-Dependent Translation in Cancer.

Cardenas, E.L.O'Rourke, R.L.Menon, A.Meagher, J.Stuckey, J.Garner, A.L.

(2023) J Med Chem 66: 10734-10745

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00917
  • Primary Citation of Related Structures:  
    8SX4

  • PubMed Abstract: 

    Eukaryotic translation initiation factor 4E (eIF4E) is an RNA-binding protein that binds to the m 7 GpppX-cap at the 5' terminus of coding mRNAs to initiate cap-dependent translation. While all cells require cap-dependent translation, cancer cells become addicted to enhanced translational capacity, driving the production of oncogenic proteins involved in proliferation, evasion of apoptosis, metastasis, and angiogenesis, among other cancerous phenotypes. eIF4E is the rate-limiting translation factor, and its activation has been shown to drive cancer initiation, progression, metastasis, and drug resistance. These findings have established eIF4E as a translational oncogene and promising, albeit challenging, anti-cancer therapeutic target. Although significant effort has been put forth toward inhibiting eIF4E, the design of cell-permeable, cap-competitive inhibitors remains a challenge. Herein, we describe our work toward solving this long-standing challenge. By employing an acyclic nucleoside phosphonate prodrug strategy, we report the synthesis of cell-permeable inhibitors of eIF4E binding to capped mRNA to inhibit cap-dependent translation.


  • Organizational Affiliation

    Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 4E
A, B
191Homo 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
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M7G
Query on M7G

Download Ideal Coordinates CCD File 
D [auth B]7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
C11 H18 N5 O11 P2
SBASPRRECYVBRF-KQYNXXCUSA-O
WXL (Subject of Investigation/LOI)
Query on WXL

Download Ideal Coordinates CCD File 
C [auth A][(~{Z})-4-[2-azanyl-7-[(5-chloranyl-1~{H}-indol-2-yl)methyl]-6-oxidanylidene-1~{H}-purin-9-yl]but-2-enyl]phosphonic acid
C18 H19 Cl N6 O4 P
JSTMWLOUXSFOCX-UPHRSURJSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.125α = 90
b = 74.328β = 97.13
c = 51.877γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASESphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM132341

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-08-23
    Changes: Data collection, Database references