1ING

INFLUENZA A SUBTYPE N2 NEURAMINIDASE COMPLEXED WITH AROMATIC BANA109 INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • Primary Citation of Related Structures:  

  • 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 p ...

    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: 
    • 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
    • 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
    • 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
    • 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.,Sect.D 51: 504


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INFLUENZA A SUBTYPE N2 NEURAMINIDASE
A, B
388Influenza A virus (strain A/Tokyo/3/1967 H2N2)Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
Find proteins for P06820 (Influenza A virus (strain A/Tokyo/3/1967 H2N2))
Go to UniProtKB:  P06820
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
ST5
Query on ST5

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Download CCD File 
A, B
4-(ACETYLAMINO)-3-[(HYDROXYACETYL)AMINO]BENZOIC ACID
C11 H12 N2 O5
CRHJDPGLFDNPOA-UHFFFAOYSA-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
FUL
Query on FUL

Download SDF File 
Download CCD File 
A
BETA-L-FUCOSE
6-DEOXY-BETA-L-GALACTOSE
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ST5IC50: >10000000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.163 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 119.420α = 90.00
b = 139.060β = 90.00
c = 139.620γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
XENGENdata reduction
X-PLORmodel building
XENGENdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-08-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance