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 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 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:  
    6CF7, 6CFG

  • 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 evaluated in clinical trials, antibodies are generally unsuited for oral delivery ...

    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

    The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HemagglutininA334Influenza A virus (A/Viet Nam/1203/2004(H5N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for Q5EP31 (Influenza A virus)
Explore Q5EP31 
Go to UniProtKB:  Q5EP31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5EP31
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HemagglutininB177Influenza A virus (A/Viet Nam/1203/2004(H5N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A8UDR1 (Influenza A virus)
Explore A8UDR1 
Go to UniProtKB:  A8UDR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8UDR1
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC, D 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EZ7
Query on EZ7

Download Ideal Coordinates CCD File 
G [auth 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 Ideal Coordinates CCD File 
E [auth A],
F [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
H [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-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 
  • R-Value Observed: 0.206 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.197α = 90
b = 102.197β = 90
c = 454.053γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR56 AI117675

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2019-03-27
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-10
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary