4XBB | pdb_00004xbb

1.85A resolution structure of Norovirus 3CL protease complex with a covalently bound dipeptidyl inhibitor diethyl [(1R,2S)-2-[(N-{[(3-chlorobenzyl)oxy]carbonyl}-3-cyclohexyl-L-alanyl)amino]-1-hydroxy-3-(2-oxo-2H-pyrrol-3-yl)propyl]phosphonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.197 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.164 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3ZRClick on this verticalbar to view details

This is version 1.5 of the entry. See complete history


Literature

Structure-Guided Design and Optimization of Dipeptidyl Inhibitors of Norovirus 3CL Protease. Structure-Activity Relationships and Biochemical, X-ray Crystallographic, Cell-Based, and In Vivo Studies.

Galasiti Kankanamalage, A.C.Kim, Y.Weerawarna, P.M.Uy, R.A.Damalanka, V.C.Mandadapu, S.R.Alliston, K.R.Mehzabeen, N.Battaile, K.P.Lovell, S.Chang, K.O.Groutas, W.C.

(2015) J Med Chem 58: 3144-3155

  • DOI: https://doi.org/10.1021/jm5019934
  • Primary Citation of Related Structures:  
    4XBB, 4XBC, 4XBD

  • PubMed Abstract: 

    Norovirus infection constitutes the primary cause of acute viral gastroenteritis. There are currently no vaccines or norovirus-specific antiviral therapeutics available for the management of norovirus infection. Norovirus 3C-like protease is essential for viral replication, consequently, inhibition of this enzyme is a fruitful avenue of investigation that may lead to the emergence of antinorovirus therapeutics. We describe herein the optimization of dipeptidyl inhibitors of norovirus 3C-like protease using iterative SAR, X-ray crystallographic, and enzyme and cell-based studies. We also demonstrate herein in vivo efficacy of an inhibitor using the murine model of norovirus infection.


  • Organizational Affiliation

    †Department of Chemistry, Wichita State University, 1845 North Fairmount Avenue, Wichita, Kansas 67260, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-LIKE PROTEASE188Norovirus Hu/1968/USMutation(s): 0 
Gene Names: ORF1
EC: 3.4.22.66
UniProt
Find proteins for Q83883 (Norovirus (strain Human/NoV/United States/Norwalk/1968/GI))
Explore Q83883 
Go to UniProtKB:  Q83883
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ83883
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3ZR
Query on 3ZR

Download Ideal Coordinates CCD File 
B [auth A]diethyl [(1R,2S)-2-[(N-{[(3-chlorobenzyl)oxy]carbonyl}-3-cyclohexyl-L-alanyl)amino]-1-hydroxy-3-(2-oxo-2H-pyrrol-3-yl)propyl]phosphonate
C28 H39 Cl N3 O8 P
MWLFTRMZFWFMSR-HFKGTQBBSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.197 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.171α = 90
b = 124.171β = 90
c = 49.969γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3ZRClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 1.1: 2015-04-22
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Advisory, Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.3: 2018-01-17
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-10-16
    Changes: Structure summary