6VH2

2.26 A resolution structure of MERS 3CL protease in complex with inhibitor 7i


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV-infected mice.

Rathnayake, A.D.Zheng, J.Kim, Y.Perera, K.D.Mackin, S.Meyerholz, D.K.Kashipathy, M.M.Battaile, K.P.Lovell, S.Perlman, S.Groutas, W.C.Chang, K.O.

(2020) Sci Transl Med 12

  • DOI: 10.1126/scitranslmed.abc5332
  • Primary Citation of Related Structures:  
    6VGY, 6VGZ, 6VH0, 6VH1, 6VH2, 6VH3, 6W2A, 6XMK

  • PubMed Abstract: 
  • Pathogenic coronaviruses are a major threat to global public health, as exemplified by severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the newly emerged SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19) ...

    Pathogenic coronaviruses are a major threat to global public health, as exemplified by severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the newly emerged SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19). We describe herein the structure-guided optimization of a series of inhibitors of the coronavirus 3C-like protease (3CLpro), an enzyme essential for viral replication. The optimized compounds were effective against several human coronaviruses including MERS-CoV, SARS-CoV, and SARS-CoV-2 in an enzyme assay and in cell-based assays using Huh-7 and Vero E6 cell lines. Two selected compounds showed antiviral effects against SARS-CoV-2 in cultured primary human airway epithelial cells. In a mouse model of MERS-CoV infection, administration of a lead compound 1 day after virus infection increased survival from 0 to 100% and reduced lung viral titers and lung histopathology. These results suggest that this series of compounds has the potential to be developed further as antiviral drugs against human coronaviruses.


    Organizational Affiliation

    Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA. kchang@vet.ksu.edu stanley-perlman@uiowa.edu bill.groutas@wichita.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Orf1a proteinA, B313Middle East respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: orf1a
EC: 2.7.7.48 (UniProt), 3.4.19.12 (UniProt), 3.4.22.69 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt)
UniProt
Find proteins for T2B9U0 (Middle East respiratory syndrome-related coronavirus)
Explore T2B9U0 
Go to UniProtKB:  T2B9U0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QZ4 (Subject of Investigation/LOI)
Query on QZ4

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]4,4-difluorocyclohexyl [(2S)-3-cyclohexyl-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]carbamate
C23 H37 F2 N3 O5
WERUFESDSMNWQU-LNLFQRSKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.028α = 90
b = 91.098β = 90
c = 100.777γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



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 StatesP30GM110761
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI109039

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references
  • Version 1.2: 2020-09-02
    Changes: Database references