6VKE

Crystal Structure of Inhibitor JNJ-40012665 in Complex with Prefusion RSV F Glycoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of 3-({5-Chloro-1-[3-(methylsulfonyl)propyl]-1H-indol-2-yl}methyl)-1-(2,2,2-trifluoroethyl)-1,3-dihydro-2H-imidazo[4,5-c]pyridin-2-one (JNJ-53718678), a Potent and Orally Bioavailable Fusion Inhibitor of Respiratory Syncytial Virus.

Vendeville, S.Tahri, A.Hu, L.Demin, S.Cooymans, L.Vos, A.Kwanten, L.Van den Berg, J.Battles, M.B.McLellan, J.S.Koul, A.Raboisson, P.Roymans, D.Jonckers, T.H.M.

(2020) J Med Chem 63: 8046-8058

  • DOI: 10.1021/acs.jmedchem.0c00226
  • Primary Citation of Related Structures:  
    6VKC, 6VKD, 6VKE

  • PubMed Abstract: 
  • Respiratory syncytial virus (RSV) is a seasonal virus that infects the lungs and airways of 64 million children and adults every year. It is a major cause of acute lower respiratory tract infection and is associated with significant morbidity and mortality ...

    Respiratory syncytial virus (RSV) is a seasonal virus that infects the lungs and airways of 64 million children and adults every year. It is a major cause of acute lower respiratory tract infection and is associated with significant morbidity and mortality. Despite the large medical and economic burden, treatment options for RSV-associated bronchiolitis and pneumonia are limited and mainly consist of supportive care. This publication covers the medicinal chemistry efforts resulting in the identification of JNJ-53718678, an orally bioavailable RSV inhibitor that was shown to be efficacious in a phase 2a challenge study in healthy adult subjects and that is currently being evaluated in hospitalized infants and adults. Cocrystal structures of several new derivatives helped in rationalizing some of the structure-activity relationship (SAR) trends observed.


    Organizational Affiliation

    Janssen Pharmaceutica NV, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Prefusion RSV F (DS-Cav1)A [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
R0S (Subject of Investigation/LOI)
Query on R0S

Download Ideal Coordinates CCD File 
C [auth F]4-(5-chloro-2-{[1-(3,4-dimethoxyphenyl)-2-oxo-1,2-dihydro-3H-imidazo[4,5-c]pyridin-3-yl]methyl}-1H-indol-1-yl)butanenitrile
C27 H24 Cl N5 O3
BVLCQPKSGBJPGE-UHFFFAOYSA-N
 Ligand Interaction
NHE
Query on NHE

Download Ideal Coordinates CCD File 
B [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 
F,
G [auth F],
H [auth F],
I [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth F],
E [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.77α = 90
b = 168.77β = 90
c = 168.77γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2020-01-20 
  • Released Date: 2020-05-27 
  • Deposition Author(s): McLellan, J.S.

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-27
    Type: Initial release
  • Version 1.1: 2020-07-01
    Changes: Database references
  • Version 1.2: 2020-08-26
    Changes: Database references