8W2E | pdb_00008w2e

SARS-CoV-2 M protein dimer in complex with JNJ-9676 and Fab-B


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A small-molecule SARS-CoV-2 inhibitor targeting the membrane protein.

Van Damme, E.Abeywickrema, P.Yin, Y.Xie, J.Jacobs, S.Mann, M.K.Doijen, J.Miller, R.Piassek, M.Marsili, S.Subramanian, M.Gottlieb, L.Abdelnabi, R.Van Gool, M.Van den Broeck, N.De Pauw, I.Diels, A.Vermeulen, P.Temmerman, K.Scobey, T.Mattocks, M.Schafer, A.Jochmans, D.De Jonghe, S.Leyssen, P.Chiu, W.Diosa Toro, M.Zwaagstra, M.Leijs, A.A.De Gruyter, H.L.M.Buyck, C.Van Den Heede, K.Jacobs, F.Van den Eynde, C.Thijs, L.Raeymaekers, V.Miller, S.Del Rosario, A.Neyts, J.Peeters, D.Baric, R.S.van Kuppeveld, F.J.M.Snijder, E.J.van Hemert, M.J.Monshouwer, M.Sharma, S.Draghia-Akli, R.Koul, A.Van Loock, M.

(2025) Nature 640: 506-513

  • DOI: https://doi.org/10.1038/s41586-025-08651-6
  • Primary Citation of Related Structures:  
    8W2E

  • PubMed Abstract: 

    The membrane (M) protein of betacoronaviruses is well conserved and has a key role in viral assembly 1,2 . Here we describe the identification of JNJ-9676, a small-molecule inhibitor targeting the coronavirus M protein. JNJ-9676 demonstrates in vitro nanomolar antiviral activity against SARS-CoV-2, SARS-CoV and sarbecovirus strains from bat and pangolin zoonotic origin. Using cryogenic electron microscopy (cryo-EM), we determined a binding pocket of JNJ-9676 formed by the transmembrane domains of the M protein dimer. Compound binding stabilized the M protein dimer in an altered conformational state between its long and short forms, preventing the release of infectious virus. In a pre-exposure Syrian golden hamster model, JNJ-9676 (25 mg per kg twice per day) showed excellent efficacy, illustrated by a significant reduction in viral load and infectious virus in the lung by 3.5 and 4 log 10 -transformed RNA copies and 50% tissue culture infective dose (TCID 50 ) per mg lung, respectively. Histopathology scores at this dose were reduced to the baseline. In a post-exposure hamster model, JNJ-9676 was efficacious at 75 mg per kg twice per day even when added at 48 h after infection, when peak viral loads were observed. The M protein is an attractive antiviral target to block coronavirus replication, and JNJ-9676 represents an interesting chemical series towards identifying clinical candidates addressing the current and future coronavirus pandemics.


  • Organizational Affiliation
    • Global Public Health R&D, Janssen Pharmaceutica, Beerse, Belgium.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Membrane protein
A, B
270SARS-CoV-2 pseudovirusMutation(s): 0 
UniProt
Find proteins for P0DTC5 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC5 
Go to UniProtKB:  P0DTC5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab B Heavy Chain
C, E
220Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab B Light Chain
D, F
225Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AE8 (Subject of Investigation/LOI)
Query on A1AE8

Download Ideal Coordinates CCD File 
G [auth A],
H [auth B]
(6S,8R)-N-(3-cyanophenyl)-5-{4-[difluoro(phenyl)methyl]phenyl}-6-methyl-4-oxo-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrazine-3-carboxamide
C28 H21 F2 N5 O2
XXXBMVUCPXBZMT-SFHVURJKSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government0000-0003-1808-9851

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Data collection, Database references
  • Version 1.2: 2025-04-23
    Changes: Data collection, Database references