6U09

Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking.

Wan, X.Yang, T.Cuesta, A.Pang, X.Balius, T.E.Irwin, J.J.Shoichet, B.K.Taunton, J.

(2020) J Am Chem Soc 142: 4960-4964

  • DOI: 10.1021/jacs.9b10377
  • Primary Citation of Related Structures:  
    6U09, 6U06

  • PubMed Abstract: 
  • Eukaryotic translation initiation factor 4E (eIF4E) binds the m7GTP cap structure at the 5'-end of mRNAs, stimulating the translation of proteins implicated in cancer cell growth and metastasis. eIF4E is a notoriously challenging target, and most of the reported inhibitors are negatively charged guanine analogues with negligible cell permeability ...

    Eukaryotic translation initiation factor 4E (eIF4E) binds the m7GTP cap structure at the 5'-end of mRNAs, stimulating the translation of proteins implicated in cancer cell growth and metastasis. eIF4E is a notoriously challenging target, and most of the reported inhibitors are negatively charged guanine analogues with negligible cell permeability. To overcome these challenges, we envisioned a covalent targeting strategy. As there are no cysteines near the eIF4E cap binding site, we developed a covalent docking approach focused on lysine. Taking advantage of a "make-on-demand" virtual library, we used covalent docking to identify arylsulfonyl fluorides that target a noncatalytic lysine (Lys162) in eIF4E. Guided by cocrystal structures, we elaborated arylsulfonyl fluoride 2 to 12 , which to our knowledge is the first covalent eIF4E inhibitor with cellular activity. In addition to providing a new tool for acutely inactivating eIF4E in cells, our computational approach may offer a general strategy for developing selective lysine-targeted covalent ligands.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin-Madison, 53711, USA. jlvanhoo@wisc.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 4E ABCD190Mus musculusMutation(s): 0 
Gene Names: Eif4e
Find proteins for P63073 (Mus musculus)
Explore P63073 
Go to UniProtKB:  P63073
NIH Common Fund Data Resources
IMPC:  MGI:95305
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EI9
Query on EI9

Download Ideal Coordinates CCD File 
A, B, C, D
3-{(1-oxo-1,2-dihydroisoquinolin-7-yl)[(pyridin-4-yl)methyl]sulfamoyl}benzene-1-sulfonyl fluoride
C21 H16 F N3 O5 S2
YZXHBGDGBOTODO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.1α = 95.5
b = 38.24β = 87.28
c = 147.79γ = 101.85
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR35 GM122481

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2020-04-08
    Changes: Database references