5KWW

Crystal Structure of Inhibitor JNJ-53718678 In Complex with Prefusion RSV F Glycoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Therapeutic efficacy of a respiratory syncytial virus fusion inhibitor.

Roymans, D.Alnajjar, S.S.Battles, M.B.Sitthicharoenchai, P.Furmanova-Hollenstein, P.Rigaux, P.Berg, J.V.D.Kwanten, L.Ginderen, M.V.Verheyen, N.Vranckx, L.Jaensch, S.Arnoult, E.Voorzaat, R.Gallup, J.M.Larios-Mora, A.Crabbe, M.Huntjens, D.Raboisson, P.Langedijk, J.P.Ackermann, M.R.McLellan, J.S.Vendeville, S.Koul, A.

(2017) Nat Commun 8: 167-167

  • DOI: 10.1038/s41467-017-00170-x
  • Primary Citation of Related Structures:  
    5KWW

  • PubMed Abstract: 
  • Respiratory syncytial virus is a major cause of acute lower respiratory tract infection in young children, immunocompromised adults, and the elderly. Intervention with small-molecule antivirals specific for respiratory syncytial virus presents an important therapeutic opportunity, but no such compounds are approved today ...

    Respiratory syncytial virus is a major cause of acute lower respiratory tract infection in young children, immunocompromised adults, and the elderly. Intervention with small-molecule antivirals specific for respiratory syncytial virus presents an important therapeutic opportunity, but no such compounds are approved today. Here we report the structure of JNJ-53718678 bound to respiratory syncytial virus fusion (F) protein in its prefusion conformation, and we show that the potent nanomolar activity of JNJ-53718678, as well as the preliminary structure-activity relationship and the pharmaceutical optimization strategy of the series, are consistent with the binding mode of JNJ-53718678 and other respiratory syncytial virus fusion inhibitors. Oral treatment of neonatal lambs with JNJ-53718678, or with an equally active close analog, efficiently inhibits established acute lower respiratory tract infection in the animals, even when treatment is delayed until external signs of respiratory syncytial virus illness have become visible. Together, these data suggest that JNJ-53718678 is a promising candidate for further development as a potential therapeutic in patients at risk to develop respiratory syncytial virus acute lower respiratory tract infection.Respiratory syncytial virus causes lung infections in children, immunocompromised adults, and in the elderly. Here the authors show that a chemical inhibitor to a viral fusion protein is effective in reducing viral titre and ameliorating infection in rodents and neonatal lambs.


    Organizational Affiliation

    Janssen Infectious Diseases and Vaccines, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fusion glycoprotein F0, Envelope glycoprotein chimeraA [auth F]568Human orthopneumovirusHuman immunodeficiency virus 1
This entity is chimeric
Mutation(s): 0 
UniProt
Find proteins for M1E1E4 (Human immunodeficiency virus 1)
Explore M1E1E4 
Go to UniProtKB:  M1E1E4
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2))
Explore P03420 
Go to UniProtKB:  P03420
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP03420M1E1E4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6YA
Query on 6YA

Download Ideal Coordinates CCD File 
N [auth F]3-[[5-chloranyl-1-(3-methylsulfonylpropyl)indol-2-yl]methyl]-1-[2,2,2-tris(fluoranyl)ethyl]imidazo[4,5-c]pyridin-2-one
C21 H20 Cl F3 N4 O3 S
GTQTUABHRCWVLL-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
B [auth F]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
NHE
Query on NHE

Download Ideal Coordinates CCD File 
C [auth F]2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth F],
E [auth F],
F,
G [auth F],
H [auth F],
D [auth F],
E [auth F],
F,
G [auth F],
H [auth F],
I [auth F],
J [auth F],
K [auth F],
L [auth F],
M [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
6YA Binding MOAD:  5KWW Kd: 7.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 41 3 2
  • Diffraction Data DOI: 10.15785/SBGRID/478 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.99α = 90
b = 169.99β = 90
c = 169.99γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-08-16
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary