8RW3 | pdb_00008rw3

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 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.217 (Depositor) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8RW3

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 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.

Macromolecule Content 

  • Total Structure Weight: 280.2 kDa 
  • Atom Count: 19,733 
  • Modeled Residue Count: 2,343 
  • Deposited Residue Count: 2,451 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.217 (Depositor) 
  • R-Value Observed: 0.219 (Depositor) 
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

View Full Validation Report



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