Crystal structure of MERS 3CL protease in complex with a m-chlorobenzyl 2-pyrrolidone inhibitor

Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.139 

Starting Model: experimental
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Structure-Guided Design of Potent Coronavirus Inhibitors with a 2-Pyrrolidone Scaffold: Biochemical, Crystallographic, and Virological Studies.

Dampalla, C.S.Kim, Y.Zabiegala, A.Howard, D.J.Nguyen, H.N.Madden, T.K.Thurman, H.A.Cooper, A.Liu, L.Battaile, K.P.Lovell, S.Chang, K.O.Groutas, W.C.

(2024) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00551
  • Primary Citation of Related Structures:  
    9ASV, 9ASW, 9ASY, 9ASZ, 9AT0, 9AT1, 9AT3, 9AT4, 9AT5, 9AT6, 9AT7, 9ATA, 9ATD, 9ATE, 9ATF, 9ATG, 9ATH, 9ATI, 9ATJ, 9ATS, 9ATT

  • PubMed Abstract: 

    Zoonotic coronaviruses are known to produce severe infections in humans and have been the cause of significant morbidity and mortality worldwide. SARS-CoV-2 was the largest and latest contributor of fatal cases, even though MERS-CoV has the highest case-fatality ratio among zoonotic coronaviruses. These infections pose a high risk to public health worldwide warranting efforts for the expeditious discovery of antivirals. Hence, we hereby describe a novel series of inhibitors of coronavirus 3CL pro embodying an N -substituted 2-pyrrolidone scaffold envisaged to exploit favorable interactions with the S3-S4 subsites and connected to an invariant Leu-Gln P 2-P1 recognition element. Several inhibitors showed nanomolar antiviral activity in enzyme and cell-based assays, with no significant cytotoxicity. High-resolution crystal structures of inhibitors bound to the 3CL pro were determined to probe and identify the molecular determinants associated with binding, to inform the structure-guided optimization of the inhibitors, and to confirm the mechanism of action of the inhibitors.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5313Middle East respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: 1a
Find proteins for K9N638 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012))
Explore K9N638 
Go to UniProtKB:  K9N638
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK9N638
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on A1AGI

Download Ideal Coordinates CCD File 
D [auth A](1R,2S)-2-({N-[({(2S)-1-[(3-chlorophenyl)methyl]-5-oxopyrrolidin-2-yl}methoxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
C26 H37 Cl N4 O9 S
Query on A1AGJ

Download Ideal Coordinates CCD File 
C [auth A](1S,2S)-2-({N-[({(2S)-1-[(3-chlorophenyl)methyl]-5-oxopyrrolidin-2-yl}methoxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
C26 H37 Cl N4 O9 S
Query on MG

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.40 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.139 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.219α = 90
b = 58.01β = 112.47
c = 49.855γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI130092
National Institutes of Health/Office of the DirectorUnited StatesS10OD030394

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release