9ECV | pdb_00009ecv

CryoEM Structure Of Respiratory Syncytial Virus Polymerase in complex with Novel Non-Nucleoside Inhibitor Compound 16


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

DNA-Encoded Library Screen Identifies Novel Series of Respiratory Syncytial Virus Polymerase Inhibitors.

Carney, S.M.Grosse, S.Yin, Y.Tran, M.T.Kalin, J.H.Jacoby, E.Fung, A.Simmons, N.Xie, X.Bhaumik, A.Carbajo, R.J.Piassek, M.Miller, R.Hu, L.Lemmens, C.Lutter, F.H.Pieters, S.Rombouts, G.Vetrano, I.Oehlrich, D.Tomaso, S.Lozada, K.Garcia, M.O.Anson, B.De Bruyn, S.Smith-Monroy, C.Neefs, J.M.Conceicao-Neto, N.Kesteleyn, B.Fino, R.Stoops, B.van Vlijmen, H.Patrick, A.N.Yu, X.Wong, V.Krosky, D.J.Abeywickrema, P.Ortiz-Meoz, R.F.Mason, S.W.Jin, Z.Sharma, S.Jonckers, T.H.M.

(2025) J Med Chem 68: 6407-6430

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02906
  • Primary Citation of Related Structures:  
    9ECV, 9ED2

  • PubMed Abstract: 

    Respiratory syncytial virus (RSV) remains a public health burden due to unmet therapeutic needs. We recently reported the discovery of a non-nucleoside inhibitor of the RSV polymerase and characterized its binding to a novel pocket within the capping domain of the polymerase. Here, we describe our strategy to diversify the chemical matter targeting this site by screening our DNA-encoded chemical libraries, leading to the discovery of a novel and potent series of molecules that inhibits RSV polymerase's biochemical activity, as well as its viral replication in cells. Structural analysis via cryo-EM revealed novel contacts made within the capping domain binding pocket. By leveraging these structural insights for preliminary SAR exploration, we generated analogues for which potency and metabolic stability were improved more than 60- and 40-fold, respectively, over the initial hit. This work provides a path forward for further advanced SAR exploration and development of therapeutics against RSV.


  • Organizational Affiliation
    • Janssen Research & Development, LLC, Johnson & Johnson Company, Spring House, Pennsylvania 19002, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase L2,201human respiratory syncytial virusMutation(s): 0 
EC: 2.7.7.48 (PDB Primary Data), 3.6.1 (PDB Primary Data), 2.7.7.88 (PDB Primary Data), 2.1.1.375 (PDB Primary Data)
UniProt
Find proteins for P28887 (Human respiratory syncytial virus A (strain A2))
Explore P28887 
Go to UniProtKB:  P28887
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28887
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoprotein
B, C, D, E
256human respiratory syncytial virusMutation(s): 1 
UniProt
Find proteins for P03421 (Human respiratory syncytial virus A (strain A2))
Explore P03421 
Go to UniProtKB:  P03421
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03421
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Compound 16F [auth G]3synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HPE
Query on HPE
F [auth G]L-PEPTIDE LINKINGC10 H13 N O2PHE
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-24
    Type: Initial release