9DON | pdb_00009don

Crystal structure of eIF4e in complex with Compound 5-PA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 
    0.247 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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Literature

Second-Generation Cap Analogue Prodrugs for Targeting Aberrant Eukaryotic Translation Initiation Factor 4E Activity in Cancer.

Cardenas, E.L.O'Rourke, R.L.Menon, A.Vega-Hernandez, G.Meagher, J.Stuckey, J.Garner, A.L.

(2025) ACS Med Chem Lett 16: 96-100

  • DOI: https://doi.org/10.1021/acsmedchemlett.4c00466
  • Primary Citation of Related Structures:  
    9DON

  • PubMed Abstract: 

    Dysregulation of translation is a hallmark of cancer that enables rapid changes in cellular protein production to shape oncogenic phenotypes. Translation initiation is governed by the m 7 GpppX cap-binding protein eukaryotic translation initiation factor 4E (eIF4E), the rate-limiting factor of cap-dependent translation initiation. eIF4E is overexpressed in many cancers and drives the production of oncoproteins that promote tumor growth and survival. Accordingly, eIF4E has been established as an attractive albeit challenging therapeutic target. Building upon our previous work of developing cell-permeable cap analogue prodrugs that inhibit eIF4E binding to the m 7 GpppX cap, herein we disclose the design of second-generation cap analogues with alternative N -9-substituted linkers which exhibit anticancer activity in BRAF V600E mutant melanoma cell lines.


  • 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
A1A8P (Subject of Investigation/LOI)
Query on A1A8P

Download Ideal Coordinates CCD File 
D [auth B]2-[3-[[2-azanyl-7-[(5-chloranyl-1-benzofuran-2-yl)methyl]-6-oxidanylidene-1~{H}-purin-9-yl]methyl]phenyl]ethylphosphonic acid
C23 H22 Cl N5 O5 P
LOKWXOGCATZPBT-UHFFFAOYSA-O
M7G
Query on M7G

Download Ideal Coordinates CCD File 
C [auth A]7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
C11 H18 N5 O11 P2
SBASPRRECYVBRF-KQYNXXCUSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free:  0.247 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.194α = 90
b = 74.397β = 97.38
c = 52.454γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

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: 2025-01-29
    Type: Initial release