9C7Y | pdb_00009c7y

Structure Of Respiratory Syncytial Virus Polymerase in complex with JNJ-2729


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure-Activity Relationship of Oxacyclo- and Triazolo-Containing Respiratory Syncytial Virus Polymerase Inhibitors.

Tran, M.T.Grosse, S.Carbajo, R.J.Jacoby, E.Yin, Y.Yu, X.Martinez, C.Stoops, B.Cooymans, L.Hu, L.Lutter, F.H.Pieters, S.Tan, E.Alcazar, J.Roymans, D.van Vlijmen, H.Rigaux, P.Sharma, S.Jonckers, T.H.M.

(2024) ACS Med Chem Lett 15: 1549-1558

  • DOI: https://doi.org/10.1021/acsmedchemlett.4c00272
  • Primary Citation of Related Structures:  
    9C7Y

  • PubMed Abstract: 

    Despite the availability of medicines preventing respiratory syncytial virus (RSV) infection, post-exposure treatment options are needed for addressing patient's needs. RSV non-nucleoside polymerase inhibitors (NNI) have emerged as a promising asset for which our group previously disclosed JNJ-8003 with potent in vitro antiviral activity and pronounced in vivo efficacy. In this work, a structural-guided design to modify the linker vector of JNJ-8003 resulted in the identification of 2-oxacyclo pyridine-containing derivatives whose various ring closing strategies are described. In addition, bioisosteric replacement of an amide bond with triazole retained potency, and cryo-electron microscopy (cryo-EM) confirmed binding in the capping domain. Subsequent NMR conformational analysis suggested a correlation between the potency and conformations. Our efforts have fulfilled the aim of identifying linker modifications with maintained biological activity while enriching structural diversity and allowing modulations of other parameters.


  • Organizational Affiliation
    • Janssen Pharmaceutica NV, 2340 Beerse, Belgium.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase L2,201Human respiratory syncytial virus A2Mutation(s): 0 
EC: 2.7.7.48 (PDB Primary Data), 2.1.1.56 (PDB Primary Data), 2.7.7 (PDB Primary Data), 2.7.7.88 (PDB Primary Data), 3.6.1 (UniProt), 2.1.1.375 (UniProt)
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoprotein
B, C, D, E
256Human respiratory syncytial virus A2Mutation(s): 0 
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AWZ (Subject of Investigation/LOI)
Query on A1AWZ

Download Ideal Coordinates CCD File 
F [auth A](2S)-1,1,1-trifluoro-2-[5-fluoro-6-(4-fluorophenyl)-4-(2-hydroxypropan-2-yl)pyridin-2-yl]-3-[(4M)-4-(8-methoxyquinolin-6-yl)-1H-1,2,3-triazol-1-yl]propan-2-ol
C29 H24 F5 N5 O3
NMKUMDYBGSDRRI-NDEPHWFRSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-08
    Type: Initial release