7MFL | pdb_00007mfl

Structure of the Clostridium perfringens GH89 in complex with beta-HNJNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.197 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Z8VClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Iminosugar C-Glycosides Work as Pharmacological Chaperones of NAGLU, a Glycosidase Involved in MPS IIIB Rare Disease*.

Zhu, S.Jagadeesh, Y.Tran, A.T.Imaeda, S.Boraston, A.Alonzi, D.S.Poveda, A.Zhang, Y.Desire, J.Charollais-Thoenig, J.Demotz, S.Kato, A.Butters, T.D.Jimenez-Barbero, J.Sollogoub, M.Bleriot, Y.

(2021) Chemistry 27: 11291-11297

  • DOI: https://doi.org/10.1002/chem.202101408
  • Primary Citation of Related Structures:  
    7MFK, 7MFL

  • PubMed Abstract: 

    Mucopolysaccharidosis type IIIB is a devastating neurological disease caused by a lack of the lysosomal enzyme, α-N-acetylglucosaminidase (NAGLU), leading to a toxic accumulation of heparan sulfate. Herein we explored a pharmacological chaperone approach to enhance the residual activity of NAGLU in patient fibroblasts. Capitalizing on the three-dimensional structures of two modest homoiminosugar-based NAGLU inhibitors in complex with bacterial homolog of NAGLU, CpGH89, we have synthesized a library of 17 iminosugar C-glycosides mimicking N-acetyl-D-glucosamine and bearing various pseudo-anomeric substituents of both α- and β-configuration. Elaboration of the aglycon moiety results in low micromolar selective inhibitors of human recombinant NAGLU, but surprisingly it is the non-functionalized and wrongly configured β-homoiminosugar that was proved to act as the most promising pharmacological chaperone, promoting a 2.4 fold activity enhancement of mutant NAGLU at its optimal concentration.


  • Organizational Affiliation

    Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, UMR 8232, 4 place Jussieu, 75005, Paris, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-N-acetylglucosaminidase family protein899Clostridium perfringens ATCC 13124Mutation(s): 0 
Gene Names: CPF_0859
UniProt
Find proteins for A0A0H2YU91 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A))
Explore A0A0H2YU91 
Go to UniProtKB:  A0A0H2YU91
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2YU91
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Z8V (Subject of Investigation/LOI)
Query on Z8V

Download Ideal Coordinates CCD File 
J [auth A]N-[(2R,3S,4R,5R,6R)-4,5-dihydroxy-2,6-bis(hydroxymethyl)piperidin-3-yl]acetamide
C9 H18 N2 O5
GYKHMAHAJKZLAT-KVEIKIFDSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A],
K [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.197 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91α = 90
b = 91β = 90
c = 252.812γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Z8VClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2021-08-04
    Changes: Database references
  • Version 1.2: 2021-08-11
    Changes: Advisory, Database references
  • Version 1.3: 2021-08-18
    Changes: Database references
  • Version 1.4: 2023-10-18
    Changes: Data collection, Refinement description