9N99 | pdb_00009n99

SARS-CoV-2 Main protease in complex with AVI-8122


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.230 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9N99

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Identification of a Potent Pan-Coronaviral Main Protease Inhibitor.

Chen, P.Strunk, U.Arutyunova, E.Lu, J.Chen, S.A.Demmon, S.Maplethorpe, C.Kandadai, A.S.Shields, J.Saffran, H.A.Lamer, T.Fischer, C.Van Oers, T.J.Turner, Z.Leong, P.Iyyathurai, J.Young, H.S.Bai, B.Vederas, J.C.Nieman, J.A.Joyce, M.A.Tyrrell, D.L.Lemieux, M.J.

(2026) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.6c00645
  • Primary Citation Related Structures: 
    9N98, 9N99, 9N9T, 9N9U, 9N9V, 9NA0

  • PubMed Abstract: 

    The global impact of SARS-CoV-2 and the continued emergence of zoonotic coronaviruses underscore the urgent need for broad-spectrum antivirals for pandemic preparedness. Herein, we report AVI8122 , a covalent pan-coronaviral inhibitor that targets 19 M pro s across the α, β, γ, and δ genera, encompassing bat, human, and other animal coronaviruses. AVI8122 exhibits low nanomolar potency and favorable pharmacokinetics in mice. Structural studies reveal that AVI8122 forms a covalent bond with the catalytic cysteine and maintains conserved interactions within the active sites of these M pro s. In cellulo , AVI8122 efficiently inhibited the replication of SARS-CoV-2 and its variants of concern as well as the activity of M pro s from all four genera. Furthermore, in mouse models, AVI8122 conferred dose-dependent protection against a lethal SARS-CoV-2 infection. Our findings position AVI8122 as an early lead compound and a tractable structural starting point for the development of broad-spectrum antivirals against future coronavirus spillover threats.


  • Organizational Affiliation
    • Department of Biochemistry, University of Alberta, Edmonton, T6G 2H7 AB, Canada.

Macromolecule Content 

  • Total Structure Weight: 68.6 kDa 
  • Atom Count: 5,104 
  • Modeled Residue Count: 607 
  • Deposited Residue Count: 612 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5
A, B
306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22.69
UniProt
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BWH

Query on A1BWH



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
N-[(2S)-3-cyclopropyl-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopiperidin-3-yl]butan-2-yl}amino)-1-oxopropan-2-yl]-7-fluoro-1H-indole-2-carboxamide
C24 H31 F N4 O5
SXZDNPUJTOHKJI-TXJVSEOTSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.230 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.291α = 90
b = 53.67β = 101.26
c = 112.845γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-18
    Type: Initial release
  • Version 1.1: 2026-07-22
    Changes: Database references
  • Version 1.2: 2026-07-29
    Changes: Database references