Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 92.09 kDa 
• Atom Count: 6430 
• Modelled Residue Count: 776 
• Deposited Residue Count: 776 
• Unique protein chains: 1

1IVC

STRUCTURES OF AROMATIC INHIBITORS OF INFLUENZA VIRUS NEURAMINIDASE

• PDB DOI: 10.2210/pdb1IVC/pdb

• Classification: HYDROLASE (O-GLYCOSYL)
• Organism(s): Influenza A virus (A/Tokyo/3/1967(H2N2))
• Mutation(s): No 


• Deposited: 1994-12-12 Released: 1995-03-31 
• Deposition Author(s): Jedrzejas, M.J., Luo, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work: 0.204 
• R-Value Observed: 0.204 

Literature

Structures of aromatic inhibitors of influenza virus neuraminidase.

Jedrzejas, M.J., Singh, S., Brouillette, W.J., Laver, W.G., Air, G.M., Luo, M.

(1995) Biochemistry 34: 3144-3151

• PubMed: 7880809 
• DOI: 10.1021/bi00010a003
• Primary Citation of Related Structures:  
  1IVB, 1IVC, 1IVD, 1IVE, 1IVF, 1IVG


• PubMed Abstract: 
  

Neuraminidase (NA), a surface glycoprotein of influenza virus, is a potential target for design of antiinfluenza agents. The crystal structure of influenza virus neuraminidase showed that in the active site 11 residues are universally conserved among all strains known so far. Several potent inhibitors based on the carbohydrate compound 2-deoxy-2,3-didehydro-D-N-acetylneuraminic acid (DANA) have been shown to bind to the conserved active site and to reduce virus infection in animals when administered by nasal spray. Inhibitors of this type are, however, rapidly excreted from physiological systems and may not be effective in order to provide long-time protection. A new class of specific NA inhibitors, which are benzoic acid derivatives, has been designed on the basis of the three-dimensional structure of the NA-DANA complex and modeling of derivatives of 4-(acetylamino)benzoic acid in the NA active site. Intermediates were synthesized and were shown to moderately inhibit the NA activity and to bind to the NA active site as predicted. These rudimentary inhibitors, 4-(acetylamino)-3-hydroxy-5-nitrobenzoic acid, 4-(acetylamino)-3-hydroxy-5-aminobenzoic acid, and 4-(acetylamino)-3-aminobenzoic acid, and their X-ray structures in complexes with N2 (A/Tokyo/3/67) and B/Lee/40 neuraminidases have been analyzed. The coordinates of such inhibitors complexed with NA were used as the starting model for further design of more potent benzoic acid inhibitors. Because the active site residues of NA are invariant, the designed aromatic inhibitors have the potential to become an antiviral drug against all strains of influenza virus.

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Related Citations: 

• Structure-Based Inhibitors of Influenza Viral Neuraminidase. A Benzoic Acid Lead with Novel Interaction
  Singh, S., Jedrzejas, M.J., Air, G.M., Luo, M., Laver, W.G., Brouillette, W.J.
  () To be published --: --

• Benzoic Acid Inhibitors of Influenza Virus Neuraminidase
  Luo, M., Jedrzejas, M.J., Singh, S., White, C.L., Brouillette, W.J., Air, G.M., Laver, W.G.
  () To be published --: --

• Three-Dimensional Structure of the Neuraminidase of Influenza Virus A(Slash)Tokyo(Slash)3(Slash)67 at 2.2 Angstroms Resolution
  Varghese, J.N., Colman, P.M.
  (1991) J Mol Biol 221: 473

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Organizational Affiliation: 

Department of Microbiology, University of Alabama at Birmingham 35294.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INFLUENZA A SUBTYPE N2 NEURAMINIDASE	A, B	388	Influenza A virus (A/Tokyo/3/1967(H2N2))	Mutation(s): 0  Gene Names: NA EC: 3.2.1.18
UniProt
Find proteins for P06820 (Influenza A virus (strain A/Tokyo/3/1967 H2N2)) Explore P06820  Go to UniProtKB:  P06820

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, F, G, J	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86566TX GlyCosmos:  G86566TX GlyGen:  G86566TX

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	E, I	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G19158MO GlyCosmos:  G19158MO GlyGen:  G19158MO

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ST2	L [auth A], N [auth B]	4-(ACETYLAMINO)-5-AMINO-3-HYDROXYBENZOIC ACID C9 H10 N2 O4 CALDTVBHJMBRTM-UHFFFAOYSA-N
CA	K [auth A], M [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work: 0.204 
• R-Value Observed: 0.204 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.35	α = 90
b = 139.72	β = 90
c = 140.23	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-12-12 
• Released Date: 1995-03-31 
Deposition Author(s): Jedrzejas, M.J., Luo, M.

Revision History  

• Version 1.0: 1995-03-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Structure summary