9ED2 | pdb_00009ed2

CryoEM map of Respiratory Syncytial Virus Polymerase with Non-Nucleoside Inhibitor compound 21

• PDB DOI: https://doi.org/10.2210/pdb9ED2/pdb
• EM Map EMD-47931: EMDB EMDataResource

• Classification: VIRAL PROTEIN/INHIBITOR
• Organism(s): human respiratory syncytial virus, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2024-11-15 Released: 2025-09-24 
• Deposition Author(s): Yin, Y., Tran, M.T., Yu, X., Jonckers, T., Carney, S.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.72 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 40042938 
• DOI: https://doi.org/10.1021/acs.jmedchem.4c02906
• Primary Citation 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.
Janssen Pharmaceutica N.V., Beerse 2340, Belgium.
Janssen Research & Development, LLC, Johnson & Johnson Company, Brisbane, California 94005, United States.
Janssen Research & Development, LLC, Johnson & Johnson Company, San Diego, California 92121, United States.
Janssen-Cilag, S.A. Río Jarama, 75A, Toledo 45007, Spain.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 371.11 kDa 
• Atom Count: 13,558 
• Modeled Residue Count: 1,676 
• Deposited Residue Count: 3,228 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase L	A	2,201	human respiratory syncytial virus	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoprotein	B, C, D, E	256	human respiratory syncytial virus	Mutation(s): 1
UniProt
Find proteins for P03421 (Human respiratory syncytial virus A (strain A2)) Explore P03421  Go to UniProtKB:  P03421

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Compound 21	F [auth G]	3	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1BIT	F [auth G]	D-PEPTIDE LINKING	C9 H17 N O2		--
A1BIU	F [auth G]	L-PEPTIDE LINKING	C8 H8 Cl N O2		--
HPE	F [auth G]	L-PEPTIDE LINKING	C10 H13 N O2		PHE

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.72 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-09-24 
Deposition Author(s): Yin, Y., Tran, M.T., Yu, X., Jonckers, T., Carney, S.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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