9C7W | pdb_00009c7w

human OC43 Main Protease (1-303) in complex with potent inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 
    0.246 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Identification of Potent, Broad-Spectrum Coronavirus Main Protease Inhibitors for Pandemic Preparedness.

Barkan, D.T.Garland, K.Zhang, L.Eastman, R.T.Hesse, M.Knapp, M.Ornelas, E.Tang, J.Cortopassi, W.A.Wang, Y.King, F.Jia, W.Nguyen, Z.Frank, A.O.Chan, R.Fang, E.Fuller, D.Busby, S.Carias, H.Donahue, K.Tandeske, L.Diagana, T.T.Jarrousse, N.Moser, H.Sarko, C.Dovala, D.Moquin, S.Marx, V.M.

(2024) J Med Chem 67: 17454-17471

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01404
  • Primary Citation of Related Structures:  
    9C7W, 9C80, 9C8Q

  • PubMed Abstract: 

    The COVID-19 pandemic highlights the ongoing risk of zoonotic transmission of coronaviruses to global health. To prepare for future pandemics, it is essential to develop effective antivirals targeting a broad range of coronaviruses. Targeting the essential and clinically validated coronavirus main protease (M pro ), we constructed a structurally diverse M pro panel by clustering all known coronavirus sequences by M pro active site sequence similarity. Through screening, we identified a potent covalent inhibitor that engaged the catalytic cysteine of SARS-CoV-2 Mpro and used structure-based medicinal chemistry to develop compounds in the pyrazolopyrimidine sulfone series that exhibit submicromolar activity against multiple M pro homologues. Additionally, we solved the first X-ray cocrystal structure of M pro from the human-infecting OC43 coronavirus, providing insights into potency differences among compound-target pairs. Overall, the chemical compounds described in this study serve as starting points for the development of antivirals with broad-spectrum activity, enhancing our preparedness for emerging human-infecting coronaviruses.


  • Organizational Affiliation
    • Discovery Sciences, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ORF1ab polyprotein
A, B, C, D
298Human coronavirus OC43Mutation(s): 1 
Gene Names: Pp1ab
UniProt
Find proteins for U3M7V0 (Human coronavirus OC43)
Explore U3M7V0 
Go to UniProtKB:  U3M7V0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU3M7V0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free:  0.246 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.245α = 90
b = 129.805β = 90
c = 140.074γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Database references