8RW3

Crystal Structure of Agd31B, alpha-transglucosylase, complexed with a non-covalent 1,2- Cyclophellitol aziridine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Conformational and Electronic Variations in 1,2- and 1,5a-Cyclophellitols and their Impact on Retaining alpha-Glucosidase Inhibition.

Ofman, T.P.Heming, J.J.A.Nin-Hill, A.Kullmer, F.Moran, E.Bennett, M.Steneker, R.Klein, A.M.Ruijgrok, G.Kok, K.Armstrong, Z.W.B.Aerts, J.M.F.G.van der Marel, G.A.Rovira, C.Davies, G.J.Artola, M.Codee, J.D.C.Overkleeft, H.S.

(2024) Chemistry 30: e202400723-e202400723

  • DOI: https://doi.org/10.1002/chem.202400723
  • Primary Citation of Related Structures:  
    8RVK, 8RW3

  • PubMed Abstract: 

    Glycoside hydrolases (glycosidases) take part in myriad biological processes and are important therapeutic targets. Competitive and mechanism-based inhibitors are useful tools to dissect their biological role and comprise a good starting point for drug discovery. The natural product, cyclophellitol, a mechanism-based, covalent and irreversible retaining β-glucosidase inhibitor has inspired the design of diverse α- and β-glycosidase inhibitor and activity-based probe scaffolds. Here, we sought to deepen our understanding of the structural and functional requirements of cyclophellitol-type compounds for effective human α-glucosidase inhibition. We synthesized a comprehensive set of α-configured 1,2- and 1,5a-cyclophellitol analogues bearing a variety of electrophilic traps. The inhibitory potency of these compounds was assessed towards both lysosomal and ER retaining α-glucosidases. These studies revealed the 1,5a-cyclophellitols to be the most potent retaining α-glucosidase inhibitors, with the nature of the electrophile determining inhibitory mode of action (covalent or non-covalent). DFT calculations support the ability of the 1,5a-cyclophellitols, but not the 1,2-congeners, to adopt conformations that mimic either the Michaelis complex or transition state of α-glucosidases.


  • Organizational Affiliation

    Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oligosaccharide 4-alpha-D-glucosyltransferaseA [auth C],
B [auth A],
C [auth B]
817Cellvibrio japonicus Ueda107Mutation(s): 0 
Gene Names: agd31BCJA_3248
EC: 2.4.1.161
UniProt
Find proteins for B3PEE6 (Cellvibrio japonicus (strain Ueda107))
Explore B3PEE6 
Go to UniProtKB:  B3PEE6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3PEE6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
J [auth C],
P [auth A],
W [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
GDQ (Subject of Investigation/LOI)
Query on GDQ

Download Ideal Coordinates CCD File 
D [auth C],
L [auth A],
T [auth B]
(1~{S},2~{R},3~{R},4~{R},6~{S})-4-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3-diol
C7 H13 N O3
JACJTGDBUDQHPY-VOQCIKJUSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth B]
F [auth C]
G [auth C]
H [auth C]
K [auth C]
AA [auth B],
F [auth C],
G [auth C],
H [auth C],
K [auth C],
N [auth A],
O [auth A],
Q [auth A],
S [auth A],
U [auth B],
X [auth B],
Y [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
OXL
Query on OXL

Download Ideal Coordinates CCD File 
E [auth C],
R [auth A],
V [auth B]
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth C],
M [auth A],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 197.02α = 90
b = 341.249β = 90
c = 102.805γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-06-12
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Structure summary