Structure of human coronavirus NL63 main protease in complex with the alpha-ketoamide (S)-N-benzyl-3-((S)-2-cinnamamido-3-phenylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide (cinnamoyl-phenylalanine-GlnLactam-CO-CO-NH-benzyl)

Experimental Data Snapshot

  • Resolution: 2.95 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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Alpha-ketoamides as broad-spectrum inhibitors of coronavirus and enterovirus replication Structure-based design, synthesis, and activity assessment.

Zhang, L.Lin, D.Kusov, Y.Nian, Y.Ma, Q.Wang, J.von Brunn, A.Leyssen, P.Lanko, K.Neyts, J.de Wilde, A.H.Snijder, E.J.Liu, H.Hilgenfeld, R.

(2020) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01828
  • Primary Citation of Related Structures:  
    6FV1, 6FV2

  • PubMed Abstract: 

    The main protease of coronaviruses and the 3C protease of enteroviruses share a similar active-site architecture and a unique requirement for glutamine in the P1 position of the substrate. Because of their unique specificity and essential role in viral polyprotein processing, these proteases are suitable targets for the development of antiviral drugs. In order to obtain near-equipotent, broad-spectrum antivirals against alphacoronaviruses, betacoronaviruses, and enteroviruses, we pursued a structure-based design of peptidomimetic α-ketoamides as inhibitors of main and 3C proteases. Six crystal structures of protease-inhibitor complexes were determined as part of this study. Compounds synthesized were tested against the recombinant proteases as well as in viral replicons and virus-infected cell cultures; most of them were not cell-toxic. Optimization of the P2 substituent of the α-ketoamides proved crucial for achieving near-equipotency against the three virus genera. The best near-equipotent inhibitors, 11u (P2 = cyclopentylmethyl) and 11r (P2 = cyclohexylmethyl), display low-micromolar EC 50 values against enteroviruses, alphacoronaviruses, and betacoronaviruses in cell cultures. In Huh7 cells, 11r exhibits three-digit picomolar activity against the Middle East Respiratory Syndrome coronavirus.

  • Organizational Affiliation

    Max von Pettenkofer Institute, Ludwig-Maximilians-University Munich, 80336 Munich, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase
A, B, C
306Human coronavirus NL63Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22
Find proteins for P0C6X5 (Human coronavirus NL63)
Explore P0C6X5 
Go to UniProtKB:  P0C6X5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6X5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.95 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.115α = 90
b = 211.044β = 90
c = 115.63γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Center for Infection Research (DZIF)GermanyTTU 01.803

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2020-03-04
    Changes: Database references
  • Version 1.2: 2021-04-28
    Changes: Source and taxonomy, Structure summary