9BJM | pdb_00009bjm

Crystal Structure of Inhibitor 5c in Complex with Prefusion RSV F Glycoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 
    0.203 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Spiro-Azetidine Oxindoles as Long-Acting Injectables for Pre-Exposure Prophylaxis against Respiratory Syncytial Virus Infections.

Kesteleyn, B.Herschke, F.Darville, N.Stoops, B.Jacobs, T.Jacoby, E.Shaffer, P.Lammens, L.Van Rompaey, D.Matcha, K.Martinez Lamenca, C.Coesemans, E.Hache, G.Pieters, S.Lecomte, M.Hu, L.Demin, S.Milligan, C.Abeywickrema, P.De Bruyn, S.Van Den Berg, J.Ysebaert, N.De Zwart, L.Najera, I.Rigaux, P.Roymans, D.Jonckers, T.H.M.

(2024) J Med Chem 67: 10986-11002

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00514
  • Primary Citation Related Structures: 
    9BJM

  • PubMed Abstract: 

    Respiratory syncytial virus (RSV) is a major cause of hospitalization in infants, the elderly, and immune-compromised patients. While a half-life extended monoclonal antibody and 2 vaccines have recently been approved for infants and the elderly, respectively, options to prevent disease in immune-compromised patients are still needed. Here, we describe spiro-azetidine oxindoles as small molecule RSV entry inhibitors displaying favorable potency, developability attributes, and long-acting PK when injected as an aqueous suspension, suggesting their potential to prevent complications following RSV infection over a period of 3 to 6 months with 1 or 2 long-acting intramuscular (IM) or subcutaneous (SC) injections in these immune-compromised patients.


  • Organizational Affiliation
    • Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, Beerse 2340, Belgium.

Macromolecule Content 

  • Total Structure Weight: 63.75 kDa 
  • Atom Count: 3,673 
  • Modeled Residue Count: 432 
  • Deposited Residue Count: 568 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Prefusion RSV F (DS-CAV1),Envelope glycoprotein568human respiratory syncytial virusHuman immunodeficiency virus 1
This entity is chimeric
Mutation(s): 0 
UniProt
Find proteins for M1E1E4 (Human immunodeficiency virus type 1)
Explore M1E1E4 
Go to UniProtKB:  M1E1E4
Find proteins for W8RJF9 (Human respiratory syncytial virus)
Explore W8RJF9 
Go to UniProtKB:  W8RJF9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsM1E1E4W8RJF9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1APZ
(Subject of Investigation/LOI)

Query on A1APZ



Download:Ideal Coordinates CCD File
B [auth A]1'-{[5-chloro-1-(4,4,4-trifluorobutyl)-1H-1,3-benzimidazol-2-yl]methyl}-1-(methanesulfonyl)spiro[azetidine-3,3'-indol]-2'(1'H)-one
C23 H22 Cl F3 N4 O3 S
FGAFKLPJKPDQGL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free:  0.203 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.018α = 90
b = 170.018β = 90
c = 170.018γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata 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: 2024-07-10
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Structure summary