1ING

INFLUENZA A SUBTYPE N2 NEURAMINIDASE COMPLEXED WITH AROMATIC BANA109 INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Work: 0.163 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structure-based inhibitors of influenza virus sialidase. A benzoic acid lead with novel interaction.

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

(1995) J Med Chem 38: 3217-3225

  • DOI: 10.1021/jm00017a005
  • Primary Citation of Related Structures:  
    1INF, 1ING, 1INH

  • PubMed Abstract: 
  • Influenza virus sialidase is a surface enzyme that is essential for infection of the virus. The catalytic site is highly conserved among all known influenza variants, suggesting that this protein is a suitable target for drug intervention. The most potent known inhibitors are analogs of 2-deoxy-2,3-didehydro-N-acetylneuraminic acid (Neu5Ac2en), particularly the 4-guanidino derivative (4-guanidino-Neu5Ac2en) ...

    Influenza virus sialidase is a surface enzyme that is essential for infection of the virus. The catalytic site is highly conserved among all known influenza variants, suggesting that this protein is a suitable target for drug intervention. The most potent known inhibitors are analogs of 2-deoxy-2,3-didehydro-N-acetylneuraminic acid (Neu5Ac2en), particularly the 4-guanidino derivative (4-guanidino-Neu5Ac2en). We utilized the benzene ring of 4-(N-acetylamino)benzoic acids as a cyclic template to substitute for the dihydropyran ring of Neu5Ac2en. In this study several 3-(N-acylamino) derivatives were prepared as potential replacements for the glycerol side chain of Neu5Ac2en, and some were found to interact with the same binding subsite of sialidase. Of greater significance was the observation that the 3-guanidinobenzoic acid derivative (equivalent to the 4-guanidino grouping of 4-guanidino-Neu5Ac2en), the most potent benzoic acid inhibitor of influenza sialidase thus far identified (IC50 = 10 microM), occupied the glycerol-binding subsite on sialidase as opposed to the guanidino-binding subsite. This benzoic acid derivative thus provides a new compound that interacts in a novel manner with the catalytic site of influenza sialidase.


    Related Citations: 
    • 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.
      (1995) Acta Crystallogr D Biol Crystallogr 51: 504
    • 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.
      (1995) J Med Chem 38: 3217
    • 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
    • Three-Dimensional Structure of the Neuraminidase of Influenza Virus A/Tokyo/3/67 at 2.2 A Resolution
      Varghese, J.N., Colman, P.M.
      (1991) J Mol Biol 221: 473

    Organizational Affiliation

    Department of Chemistry, University of Alabama at Birmingham 35294, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
INFLUENZA A SUBTYPE N2 NEURAMINIDASEA, B388Influenza A virusMutation(s): 0 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06820
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC, F, G, J 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
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-glucopyranoseD 4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G86566TX
GlyCosmos:  G86566TX
GlyGen:  G86566TX
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
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-glucopyranoseE, I 6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G19158MO
GlyCosmos:  G19158MO
GlyGen:  G19158MO
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
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-glucopyranoseH 4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G32152BH
GlyCosmos:  G32152BH
GlyGen:  G32152BH
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ST5
Query on ST5

Download Ideal Coordinates CCD File 
L [auth A],
N [auth B]
4-(ACETYLAMINO)-3-[(HYDROXYACETYL)AMINO]BENZOIC ACID
C11 H12 N2 O5
CRHJDPGLFDNPOA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
K [auth A],
M [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ST5 PDBBind:  1ING IC50: 1.00e+7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Work: 0.163 
  • R-Value Observed: 0.163 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.42α = 90
b = 139.06β = 90
c = 139.62γ = 90
Software Package:
Software NamePurpose
XENGENdata collection
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-08-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    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