9IK2 | pdb_00009ik2

The co-crystal structure of SARS-CoV-2 Mpro in complex with compound H109


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.212 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structure-guided discovery of a small molecule inhibitor of SARS-CoV-2 main protease with potent in vitro and in vivo antiviral activities.

Yuan, S.Wang, J.Sang, X.Xie, Y.Feng, Y.Poon, V.K.M.Chan, C.C.S.Tsang, J.O.L.Chik, K.K.H.Zhou, J.Xu, Y.Han, P.Zheng, W.Fu, L.Huang, L.S.M.Wu, M.An, J.Yuen, K.Y.Qi, J.Huang, Z.Chan, J.F.W.

(2025) J Virol : e0100125-e0100125

  • DOI: https://doi.org/10.1128/jvi.01001-25
  • Primary Citation of Related Structures:  
    9IK2

  • PubMed Abstract: 

    The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (M pro ) is a clinically validated target for the treatment of coronavirus disease 2019 (COVID-19). Here, we report the hit-to-lead discovery of a new nitrile-based inhibitor, H135 , of SARS-CoV-2 M pro from a series of chemical modifications of a nitrile-warhead-containing compound guided by its 1.8 Å high-resolution crystal structure in complex with SARS-CoV-2 M pro . H135 exhibited potent and selective inhibition of SARS-CoV-2 M pro with IC 50 of 12.7 nM and exerted broad anti-SARS-CoV-2 activity in VeroE6-TMPRSS2 cells. Furthermore, H135 -treated golden Syrian hamsters demonstrated significantly lower respiratory tract viral burden compared with solvent-treated control hamsters. H135 may serve as a new lead for developing antiviral therapeutics for SARS-CoV-2 infection.IMPORTANCEIn this study, a structure-guided hit-to-lead strategy was employed to develop a nanomolar potent small molecule inhibitor H135 of SARS-CoV-2 M pro with strong anti-SARS-CoV-2 infection activity in cell cultures and animals. H135 may serve as a new lead for developing antiviral agents targeting the virus's main protease M pro .


  • Organizational Affiliation
    • State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
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
A1D9H (Subject of Investigation/LOI)
Query on A1D9H

Download Ideal Coordinates CCD File 
B [auth A]tert-butyl N-[(2S)-1-[[(2S)-1-[[(2S)-1-azanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-3,3-dimethyl-1-oxidanylidene-butan-2-yl]carbamate
C27 H41 N5 O5
YWXGXHNDBCVDDN-NFIWZKORSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.212 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.223α = 90
b = 106.223β = 90
c = 82.382γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
Cootmodel building
PHENIXrefinement
PHASESphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China92169208

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Structure summary
  • Version 1.2: 2025-11-26
    Changes: Database references