Room-temperature X-ray Crystal structure of SARS-CoV-2 main protease in complex with Narlaprevir

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

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Malleability of the SARS-CoV-2 3CL M pro Active-Site Cavity Facilitates Binding of Clinical Antivirals.

Kneller, D.W.Galanie, S.Phillips, G.O'Neill, H.M.Coates, L.Kovalevsky, A.

(2020) Structure 28: 1313

  • DOI: https://doi.org/10.1016/j.str.2020.10.007
  • Primary Citation of Related Structures:  
    6XCH, 6XQS, 6XQT, 6XQU

  • PubMed Abstract: 

    The COVID-19 pandemic caused by SARS-CoV-2 requires rapid development of specific therapeutics and vaccines. The main protease of SARS-CoV-2, 3CL M pro , is an established drug target for the design of inhibitors to stop the virus replication. Repurposing existing clinical drugs can offer a faster route to treatments. Here, we report on the binding mode and inhibition properties of several inhibitors using room temperature X-ray crystallography and in vitro enzyme kinetics. The enzyme active-site cavity reveals a high degree of malleability, allowing aldehyde leupeptin and hepatitis C clinical protease inhibitors (telaprevir, narlaprevir, and boceprevir) to bind and inhibit SARS-CoV-2 3CL M pro . Narlaprevir, boceprevir, and telaprevir are low-micromolar inhibitors, whereas the binding affinity of leupeptin is substantially weaker. Repurposing hepatitis C clinical drugs as COVID-19 treatments may be a useful option to pursue. The observed malleability of the enzyme active-site cavity should be considered for the successful design of specific protease inhibitors.

  • Organizational Affiliation

    National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA; Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA. Electronic address: coatesl@ornl.gov.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase
A, B
306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NNA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C36 H63 N5 O7 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.516α = 90
b = 54.473β = 101.48
c = 114.491γ = 90
Software Package:
Software NamePurpose
CrysalisProdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2020-10-28
    Changes: Database references, Structure summary
  • Version 1.2: 2020-11-18
    Changes: Database references
  • Version 1.3: 2020-12-16
    Changes: Database references
  • Version 1.4: 2021-04-14
    Changes: Derived calculations, Structure summary
  • Version 1.5: 2023-10-18
    Changes: Data collection, Database references, Refinement description