7A5X

Two copies of the catalytic domain of NanA sialidase from Streptococcus pneumoniae juxtaposed in the P212121 space group, in complex with DANA derivatized with a PEG linker on the glycerol group.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Polyvalent Transition-State Analogues of Sialyl Substrates Strongly Inhibit Bacterial Sialidases*.

Assailly, C.Bridot, C.Saumonneau, A.Lottin, P.Roubinet, B.Krammer, E.M.Francois, F.Vena, F.Landemarre, L.Alvarez Dorta, D.Deniaud, D.Grandjean, C.Tellier, C.Pascual, S.Montembault, V.Fontaine, L.Daligault, F.Bouckaert, J.Gouin, S.G.

(2021) Chemistry 27: 3142-3150

  • DOI: https://doi.org/10.1002/chem.202004672
  • Primary Citation of Related Structures:  
    7A54, 7A5X

  • PubMed Abstract: 

    Bacterial sialidases (SA) are validated drug targets expressed by common human pathogens such as Streptococcus pneumoniae, Vibrio cholerae, or Clostridium perfringens. Noncovalent inhibitors of bacterial SA capable of reaching the submicromolar level are rarely reported. In this work, multi- and polyvalent compounds are developed, based on the transition-state analogue 2-deoxy-2,3-didehydro-N-acetylneuraminic (DANA). Poly-DANA inhibits the catalytic activity of SA from S. pneumoniae (NanA) and the symbiotic microorganism B. thetaiotaomicron (BtSA) at the picomolar and low nanomolar levels (expressed in moles of molecules and of DANA, respectively). Each DANA grafted to the polymer surpasses the inhibitory potential of the monovalent analogue by more than four orders of magnitude, which represents the highest multivalent effect reported so far for an enzyme inhibition. The synergistic interaction is shown to operate exclusively in the catalytic domain, and not in the flanked carbohydrate-binding module (CBM). These results offer interesting perspectives for the multivalent inhibition of other SA families lacking a CBM, such as viral, parasitic, or human SA.


  • Organizational Affiliation

    CNRS, CEISAM UMR, 6230, Université de Nantes, 44000, Nantes, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sialidase A
A, B
498Streptococcus pneumoniaeMutation(s): 0 
Gene Names: nanA
EC: 3.2.1.18
UniProt
Find proteins for P62575 (Streptococcus pneumoniae)
Explore P62575 
Go to UniProtKB:  P62575
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62575
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R7H
Query on R7H

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
(4~{S},5~{R},6~{R})-5-acetamido-6-[(1~{R},2~{S})-3-[[1-(2-ethoxyethyl)-1,2,3-triazol-4-yl]methylsulfanyl]-1,2-bis(oxidanyl)propyl]-4-oxidanyl-oxane-2-carboxylic acid
C18 H30 N4 O8 S
AQJNARPQFNBHOK-KMIMBKNBSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
J [auth B],
K [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.203α = 90
b = 96.741β = 90
c = 226.381γ = 90
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-17-CE07-0028-03

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2021-03-03
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description