9IZB | pdb_00009izb

Crystal structure of SARS-CoV-2 main protease in complex with TMP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.253 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

An orally available M pro /TMPRSS2 bispecific inhibitor with potent anti-coronavirus efficacy in vivo.

Shuai, H.Qiao, J.Yoon, C.Zhang, G.Hou, Y.Xia, X.Wang, L.Deng, X.Wang, Y.Li, Q.Du, L.Liu, Y.Zhou, M.Wong, H.T.Hu, J.Liu, H.Hu, B.Wang, D.Su, J.Pan, Y.Ye, Y.Chen, Y.Fang, Z.Xia, Z.Chai, Y.Shi, J.Wang, Y.Zhu, T.Zhang, H.Yuan, S.Zhou, J.Chan, J.F.Yuen, K.Y.Xu, C.Lei, J.Yang, S.Chu, H.

(2025) Nat Commun 16: 6541-6541

  • DOI: https://doi.org/10.1038/s41467-025-60832-z
  • Primary Citation of Related Structures:  
    9IZB

  • PubMed Abstract: 

    Coronaviruses have caused three major endemics in the past two decades. Alarmingly, recent identification of novel zoonotic coronaviruses that caused human infections suggests the risk of future coronavirus outbreak caused by spillover infection from animal reservoirs remains high. Therefore, development of alternative therapeutic options with broad-spectrum anti-coronavirus activities are urgently needed. Here, we develop an orally available bispecific inhibitor, TMP1, which simultaneously targets key coronavirus replication protease M pro and the essential airway protease TMPRSS2. TMP1 shows broad-spectrum protection not only against different SARS-CoV-2 variants but also against multiple human-pathogenic coronaviruses in vitro. By using the K18-hACE2 transgenic mouse, hDPP4 knock-in mouse and golden Syrian hamster models, we demonstrate TMP1 cross-protects against highly-pathogenic coronaviruses (SARS-CoV-1, SARS-CoV-2 and MERS-CoV) in vivo and efficiently abrogates SARS-CoV-2 transmission. Through structural and mutagenesis studies, we confirm the direct interaction of TMP1 with M pro and TMPRSS2, and pinpoint the key sites of interactions. Importantly, TMP1 inhibits the infection of nirmatrelvir-resistant SARS-CoV-2 escape mutants. Together, our findings demonstrate the antiviral potential of the bispecific M pro /TMPRSS2 antiviral design against human-pathogenic coronaviruses and other emerging coronaviruses.


  • Organizational Affiliation
    • State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, and Pandemics Research Alliance Unit at The University of Hong Kong, Hong Kong Special Administrative Region, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
EC: 3.4.22.69
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC1 
Go to UniProtKB:  P0DTC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC1
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TMP15synthetic constructMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FP9
Query on FP9
B
L-PEPTIDE LINKINGC5 H8 F N O2PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.253 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.162α = 90
b = 53.71β = 101.26
c = 44.258γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2022YFC2303700

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-28
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Database references