4FOY

Crystal structure of the NanB sialidase from streptococcus pneumoniae in complex with 2-(Benzylammonio)ethanesulfonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Synthesis and structural characterisation of selective non-carbohydrate-based inhibitors of bacterial sialidases.

Brear, P.Telford, J.Taylor, G.L.Westwood, N.J.

(2012) Chembiochem 13: 2374-2383

  • DOI: 10.1002/cbic.201200433
  • Primary Citation of Related Structures:  
    4FOV, 4FOW, 4FOY, 4FOQ, 4FP2, 4FP3, 4FPY, 4FPO, 4FQ4, 4FPF

  • PubMed Abstract: 
  • The major human pathogen Streptococcus pneumoniae plays a key role in several disease states including septicaemia, meningitis and community-acquired pneumonia. Although vaccines against S. pneumoniae are available as prophylactics, there remains a n ...

    The major human pathogen Streptococcus pneumoniae plays a key role in several disease states including septicaemia, meningitis and community-acquired pneumonia. Although vaccines against S. pneumoniae are available as prophylactics, there remains a need to identify and characterise novel chemical entities that can treat the diseases caused by this pathogen. S. pneumoniae expresses three sialidases, enzymes that cleave sialic acid from carbohydrate-based surface molecules. Two of these enzymes, NanA and NanB, have been implicated in the pathogenesis of S. pneumoniae and are considered to be validated drug targets. Here we report our studies on the synthesis and structural characterisation of novel NanB-selective inhibitors that are inspired by the β-amino-sulfonic acid family of buffers.


    Organizational Affiliation

    Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sialidase BA697Streptococcus pneumoniaeMutation(s): 0 
Gene Names: nanBSP_1687
EC: 3.2.1.18
Find proteins for Q54727 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore Q54727 
Go to UniProtKB:  Q54727
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D53
Query on D53

Download CCD File 
A
2-(benzylamino)ethanesulfonic acid
C9 H13 N O3 S
DRWVGXPRVWLEPQ-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.318α = 90
b = 82.596β = 90
c = 117.019γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-06-21 
  • Released Date: 2012-10-31 
  • Deposition Author(s): Brear, P.

Revision History 

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2012-11-14
    Changes: Database references