4NC5

Human sialidase 2 in complex with 2,3-difluorosialic acid (covalent intermediate)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.513 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Tuning mechanism-based inactivators of neuraminidases: mechanistic and structural insights.

Buchini, S.Gallat, F.X.Greig, I.R.Kim, J.H.Wakatsuki, S.Chavas, L.M.Withers, S.G.

(2014) Angew.Chem.Int.Ed.Engl. 53: 3382-3386

  • DOI: 10.1002/anie.201309675
  • Primary Citation of Related Structures:  4NCS

  • PubMed Abstract: 
  • 3-Fluorosialosyl fluorides are inhibitors of sialidases that function by the formation of a long-lived covalent active-site adduct and have potential as therapeutics if made specific for the pathogen sialidase. Surprisingly, human Neu2 and the Trypan ...

    3-Fluorosialosyl fluorides are inhibitors of sialidases that function by the formation of a long-lived covalent active-site adduct and have potential as therapeutics if made specific for the pathogen sialidase. Surprisingly, human Neu2 and the Trypanosoma cruzi trans-sialidase are inactivated more rapidly by the reagent with an equatorial fluorine at C3 than by its axial epimer, with reactivation following the same pattern. To explore a possible stereoelectronic basis for this, rate constants for spontaneous hydrolysis of the full series of four 3-fluorosialosyl fluorides were measured, and ground-state energies for each computed. The alpha (equatorial) anomeric fluorides hydrolyze more rapidly than their beta anomers, consistent with their higher ground-state energies. However ground-state energies do not explain the relative spontaneous reactivities of the 3-fluoro-epimers. The three-dimensional structures of the two 3-fluoro-sialosyl enzyme intermediates of human Neu2 were solved, revealing key stabilizing interactions between Arg21 and the equatorial, but not the axial, fluorine. Because of changes in geometry these interactions will increase at the transition state, likely explaining the difference in reaction rates.


    Organizational Affiliation

    Department of Chemistry, University of British Columbia, Vancouver, B. C., V6T 1Z1 (Canada).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sialidase-2
A
382Homo sapiensGene Names: NEU2
EC: 3.2.1.18
Find proteins for Q9Y3R4 (Homo sapiens)
Go to Gene View: NEU2
Go to UniProtKB:  Q9Y3R4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
FSI
Query on FSI

Download SDF File 
Download CCD File 
A
5-(acetylamino)-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid
3-FLUOROSIALIC ACID
C11 H18 F N O9
ALJLGESFXXDPKH-RISWTRDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.513 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.174 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 87.408α = 90.00
b = 87.916β = 90.00
c = 92.394γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2014-04-02
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description