1L7H | pdb_00001l7h

Crystal structure of R292K mutant influenza virus neuraminidase in complex with BCX-1812


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.177 (Depositor), 0.175 (DCC) 
  • R-Value Work: 
    0.145 (Depositor), 0.146 (DCC) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Structural studies of the resistance of influenza virus neuramindase to inhibitors.

Smith, B.J.McKimm-Breshkin, J.L.McDonald, M.Fernley, R.T.Varghese, J.N.Colman, P.M.

(2002) J Med Chem 45: 2207-2212

  • DOI: https://doi.org/10.1021/jm010528u
  • Primary Citation Related Structures: 
    1L7F, 1L7G, 1L7H

  • PubMed Abstract: 

    Zanamivir and oseltamivir, specific inhibitors of influenza virus neuraminidase, have significantly different characteristics in resistance studies. In both cases resistance is known to arise through mutations in either the hemagglutinin or neuraminidase surface proteins. A new inhibitor under development by Biocryst Pharmaceuticals, BCX-1812, has both a guanidino group, as in zanamivir, and a bulky hydrophobic group, as in oseltamivir. Using influenza A/NWS/Tern/Australia/G70C/75 (H1N9), neuraminidase variants E119G and R292K have previously been selected by different inhibitors. The sensitivity of these variants to BCX-1812 has now been measured and found in both cases to be intermediate between those of zanamivir and oseltamivir. In addition, the X-ray crystal structures of the complexes of BCX-1812 with the wild type and the two mutant neuraminidases were determined. The ligand is bound in an identical manner in each structure, with a rearrangement of the side chain of E276 from its ligand-free position. A structural explanation of the mechanism of resistance of BCX-1812, relative to zanamivir and oseltamivir in particular, is provided.


  • Organizational Affiliation
    • The Walter and Eliza Hall Institute of Medical Research, P.O. Royal Melbourne Hospital, Parkville, Victoria 3050, Australia. bsmith@wehi.edu.au

Macromolecule Content 

  • Total Structure Weight: 46.3 kDa 
  • Atom Count: 3,823 
  • Modeled Residue Count: 388 
  • Deposited Residue Count: 388 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
neuraminidase388Influenza A virusMutation(s): 1 
EC: 3.2.1.18
UniProt
Find proteins for P03472 (Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9))
Explore P03472 
Go to UniProtKB:  P03472
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03472
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G46836GH
GlyCosmos: G46836GH
GlyGen: G46836GH
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCZ

Query on BCZ



Download:Ideal Coordinates CCD File
H [auth A]3-(1-ACETYLAMINO-2-ETHYL-BUTYL)-4-GUANIDINO-2-HYDROXY-CYCLOPENTANECARBOXYLIC ACID
C15 H28 N4 O4
XRQDFNLINLXZLB-CKIKVBCHSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
D [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
K [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.177 (Depositor), 0.175 (DCC) 
  • R-Value Work:  0.145 (Depositor), 0.146 (DCC) 
Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.831α = 90
b = 180.831β = 90
c = 180.831γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-05-29
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-10-27
    Changes: Database references, Structure summary
  • Version 2.2: 2024-11-13
    Changes: Data collection, Structure summary