Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 346651.88 
• Atom Count: 23457 
• Residue Count: 3024 
• Unique protein chains: 2

5T6S

Crystal structure of the A/Shanghai/2/2013 (H7N9) influenza virus hemagglutinin in complex with the antiviral drug arbidol

• DOI: 10.2210/pdb5T6S/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus
• Expression System: Trichoplusia ni


• Deposited: 2016-09-01 Released: 2017-01-04 
• Deposition Author(s): Kadam, R.U., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.250 
• R-Value Work: 0.204 

Literature

Structural basis of influenza virus fusion inhibition by the antiviral drug Arbidol.

Kadam, R.U., Wilson, I.A.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 206-214

• PubMed: 28003465 
• DOI: 10.1073/pnas.1617020114
• Primary Citation of Related Structures:  
  5T6N


• PubMed Abstract: 
  

The broad-spectrum antiviral drug Arbidol shows efficacy against influenza viruses by targeting the hemagglutinin (HA) fusion machinery. However, the structural basis of the mechanism underlying fusion inhibition by Arbidol has remained obscure, thereby hindering its further development as a specific and optimized influenza therapeutic. We determined crystal structures of Arbidol in complex with influenza virus HA from pandemic 1968 H3N2 and recent 2013 H7N9 viruses. Arbidol binds in a hydrophobic cavity in the HA trimer stem at the interface between two protomers. This cavity is distal to the conserved epitope targeted by broadly neutralizing stem antibodies and is ∼16 Å from the fusion peptide. Arbidol primarily makes hydrophobic interactions with the binding site but also induces some conformational rearrangements to form a network of inter- and intraprotomer salt bridges. By functioning as molecular glue, Arbidol stabilizes the prefusion conformation of HA that inhibits the large conformational rearrangements associated with membrane fusion in the low pH of the endosome. This unique binding mode compared with the small-molecule inhibitors of other class I fusion proteins enhances our understanding of how small molecules can function as fusion inhibitors and guides the development of broad-spectrum therapeutics against influenza virus.

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Organizational Affiliation: 

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Hemagglutinin HA1	A, C, E, G, I, K	321	Influenza A virus	Mutation(s): 0  Gene Names: HA
Find proteins for R4NN21 (Influenza A virus) Go to UniProtKB:  R4NN21

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Hemagglutinin HA2	B, D, F, H, J, L	183	Influenza A virus	Mutation(s): 0  Gene Names: HA
Find proteins for R4NN21 (Influenza A virus) Go to UniProtKB:  R4NN21

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	J	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
75U	B, F, H, J, L	ethyl 6-bromo-4-[(dimethylamino)methyl]-5-hydroxy-1-methyl-2-[(phenylsulfanyl)methyl]-1H-indole-3-carboxylate Arbidol; Umifenovir C22 H25 Br N2 O3 S KCFYEAOKVJSACF-UHFFFAOYSA-N
BMA	C, E, I, K, L	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	A, B, C, D, E, F, G, H, I, J, K, L	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.250 
• R-Value Work: 0.204 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 67.419	α = 90.00
b = 231.490	β = 96.88
c = 127.850	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PHENIX	refinement
PHASER	phasing
Coot	model building
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-09-01 
• Released Date: 2017-01-04 
• Deposition Author(s): Kadam, R.U., Wilson, I.A.

Revision History 

• Version 1.0: 2017-01-04
  Type: Initial release
• Version 1.1: 2017-01-25
  Type: Database references