5IYT

Complex structure of EV-B93 main protease 3C with N-Ethyl 4-((1-cycloheptyl-1,2-dihydropyrazol-3-one-5-yl)-amino)-4-oxo-2Z-butenamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Irreversible inhibitors of the 3C protease of Coxsackie virus through templated assembly of protein-binding fragments.

Becker, D.Kaczmarska, Z.Arkona, C.Schulz, R.Tauber, C.Wolber, G.Hilgenfeld, R.Coll, M.Rademann, J.

(2016) Nat Commun 7: 12761-12761

  • DOI: 10.1038/ncomms12761
  • Primary Citation of Related Structures:  
    5IYT

  • PubMed Abstract: 
  • Small-molecule fragments binding to biomacromolecules can be starting points for the development of drugs, but are often difficult to detect due to low affinities. Here we present a strategy that identifies protein-binding fragments through their potential to induce the target-guided formation of covalently bound, irreversible enzyme inhibitors ...

    Small-molecule fragments binding to biomacromolecules can be starting points for the development of drugs, but are often difficult to detect due to low affinities. Here we present a strategy that identifies protein-binding fragments through their potential to induce the target-guided formation of covalently bound, irreversible enzyme inhibitors. A protein-binding nucleophile reacts reversibly with a bis-electrophilic warhead, thereby positioning the second electrophile in close proximity of the active site of a viral protease, resulting in the covalent de-activation of the enzyme. The concept is implemented for Coxsackie virus B3 3C protease, a pharmacological target against enteroviral infections. Using an aldehyde-epoxide as bis-electrophile, active fragment combinations are validated through measuring the protein inactivation rate and by detecting covalent protein modification in mass spectrometry. The structure of one enzyme-inhibitor complex is determined by X-ray crystallography. The presented warhead activation assay provides potent non-peptidic, broad-spectrum inhibitors of enteroviral proteases.


    Organizational Affiliation

    Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Straße 2+4, 14195 Berlin, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EV-B93 main protease 3CA, B191Echovirus 1 (strain Farouk / ATCC VR-1038)Mutation(s): 1 
EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (UniProt)
UniProt
Find proteins for O91734 (Echovirus 1 (strain Human/Egypt/Farouk/1951))
Explore O91734 
Go to UniProtKB:  O91734
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NZN
Query on NZN

Download Ideal Coordinates CCD File 
C [auth B]N-Ethyl 4-((1-cycloheptyl-1,2-dihydropyrazol-3-one-5-yl)-amino)-4-oxo-butanamide
C16 H26 N4 O3
LPNCMHPJRSJOIM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.46α = 90
b = 52.33β = 103.73
c = 62.27γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-10-12
    Changes: Database references