6CFG

Crystal structure of the A/Vietnam/1203/2004 (H5N1) influenza virus hemagglutinin in complex with small molecule JNJ4796


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A small-molecule fusion inhibitor of influenza virus is orally active in mice.

van Dongen, M.J.P.Kadam, R.U.Juraszek, J.Lawson, E.Brandenburg, B.Schmitz, F.Schepens, W.B.G.Stoops, B.van Diepen, H.A.Jongeneelen, M.Tang, C.Vermond, J.van Eijgen-Obregoso Real, A.Blokland, S.Garg, D.Yu, W.Goutier, W.Lanckacker, E.Klap, J.M.Peeters, D.C.G.Wu, J.Buyck, C.Jonckers, T.H.M.Roymans, D.Roevens, P.Vogels, R.Koudstaal, W.Friesen, R.H.E.Raboisson, P.Dhanak, D.Goudsmit, J.Wilson, I.A.

(2019) Science 363: --

  • DOI: 10.1126/science.aar6221
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Recent characterization of broadly neutralizing antibodies (bnAbs) against influenza virus identified the conserved hemagglutinin (HA) stem as a target for development of universal vaccines and therapeutics. Although several stem bnAbs are being eval ...

    Recent characterization of broadly neutralizing antibodies (bnAbs) against influenza virus identified the conserved hemagglutinin (HA) stem as a target for development of universal vaccines and therapeutics. Although several stem bnAbs are being evaluated in clinical trials, antibodies are generally unsuited for oral delivery. Guided by structural knowledge of the interactions and mechanism of anti-stem bnAb CR6261, we selected and optimized small molecules that mimic the bnAb functionality. Our lead compound neutralizes influenza A group 1 viruses by inhibiting HA-mediated fusion in vitro, protects mice against lethal and sublethal influenza challenge after oral administration, and effectively neutralizes virus infection in reconstituted three-dimensional cell culture of fully differentiated human bronchial epithelial cells. Cocrystal structures with H1 and H5 HAs reveal that the lead compound recapitulates the bnAb hotspot interactions.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.,Janssen Infectious Diseases and Vaccines, Janssen Research & Discovery, Turnhoutseweg 30, Beerse, Belgium.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, Leiden, Netherlands. mvandon@its.jnj.com wilson@scripps.edu.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. mvandon@its.jnj.com wilson@scripps.edu.,Janssen Infectious Diseases and Vaccines, Janssen Research & Development, Archimedesweg 4-6, Leiden, Netherlands.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.,Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, Beerse, Belgium.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, Leiden, Netherlands.,Discovery Sciences, Janssen Research & Development, 1400 McKean Rd., Spring House, PA, USA.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
A
334Influenza A virusMutation(s): 0 
Gene Names: HA
Find proteins for Q5EP31 (Influenza A virus)
Go to UniProtKB:  Q5EP31
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
B
177Influenza A virusMutation(s): 0 
Gene Names: HA
Find proteins for A8UDR1 (Influenza A virus)
Go to UniProtKB:  A8UDR1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download SDF File 
Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EZ7
Query on EZ7

Download SDF File 
Download CCD File 
B
N-[2-(2-{4-[(R)-(2-methyl-2H-tetrazol-5-yl)(phenyl)methyl]piperazine-1-carbonyl}pyridin-4-yl)-1,3-benzoxazol-5-yl]acetamide
C28 H27 N9 O3
VMAAUIZLAZYALS-RUZDIDTESA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.204 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 102.197α = 90.00
b = 102.197β = 90.00
c = 454.053γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR56 AI117675

Revision History 

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2019-03-27
    Type: Data collection, Database references
  • Version 1.2: 2019-04-10
    Type: Author supporting evidence, Data collection