1CQQ

TYPE 2 RHINOVIRUS 3C PROTEASE WITH AG7088 INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes.

Matthews, D.A.Dragovich, P.S.Webber, S.E.Fuhrman, S.A.Patick, A.K.Zalman, L.S.Hendrickson, T.F.Love, R.A.Prins, T.J.Marakovits, J.T.Zhou, R.Tikhe, J.Ford, C.E.Meador, J.W.Ferre, R.A.Brown, E.L.Binford, S.L.Brothers, M.A.DeLisle, D.M.Worland, S.T.

(1999) Proc.Natl.Acad.Sci.USA 96: 11000-11007


  • PubMed Abstract: 
  • Human rhinoviruses, the most important etiologic agents of the common cold, are messenger-active single-stranded monocistronic RNA viruses that have evolved a highly complex cascade of proteolytic processing events to control viral gene expression an ...

    Human rhinoviruses, the most important etiologic agents of the common cold, are messenger-active single-stranded monocistronic RNA viruses that have evolved a highly complex cascade of proteolytic processing events to control viral gene expression and replication. Most maturation cleavages within the precursor polyprotein are mediated by rhinovirus 3C protease (or its immediate precursor, 3CD), a cysteine protease with a trypsin-like polypeptide fold. High-resolution crystal structures of the enzyme from three viral serotypes have been used for the design and elaboration of 3C protease inhibitors representing different structural and chemical classes. Inhibitors having alpha,beta-unsaturated carbonyl groups combined with peptidyl-binding elements specific for 3C protease undergo a Michael reaction mediated by nucleophilic addition of the enzyme's catalytic Cys-147, resulting in covalent-bond formation and irreversible inactivation of the viral protease. Direct inhibition of 3C proteolytic activity in virally infected cells treated with these compounds can be inferred from dose-dependent accumulations of viral precursor polyproteins as determined by SDS/PAGE analysis of radiolabeled proteins. Cocrystal-structure-assisted optimization of 3C-protease-directed Michael acceptors has yielded molecules having extremely rapid in vitro inactivation of the viral protease, potent antiviral activity against multiple rhinovirus serotypes and low cellular toxicity. Recently, one compound in this series, AG7088, has entered clinical trials.


    Organizational Affiliation

    Agouron Pharmaceuticals, Inc., 3565 General Atomics Court, San Diego, CA 92121, USA. David.Matthews@Agouron.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TYPE 2 RHINOVIRUS 3C PROTEASE
A
180Human rhinovirus 2
Find proteins for P04936 (Human rhinovirus 2)
Go to UniProtKB:  P04936
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AG7
Query on AG7

Download SDF File 
Download CCD File 
A
4-{2-(4-FLUORO-BENZYL)-6-METHYL-5-[(5-METHYL-ISOXAZOLE-3-CARBONYL)-AMINO]-4-OXO-HEPTANOYLAMINO}-5-(2-OXO-PYRROLIDIN-3-YL)-PENTANOIC ACID ETHYL ESTER
RUPINTRIVIR, bound form
C31 H41 F N4 O7
LMIUALQNZXJHOG-IFILWLFVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 34.300α = 90.00
b = 65.700β = 90.00
c = 77.900γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
SCALEPACKdata scaling
X-PLORphasing
DENZOdata reduction
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-09-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Advisory, Experimental preparation