7P4C | pdb_00007p4c

Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31, in complex with noncovalent Cyclophellitol Sulfamidate probe KK131


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 
    0.229 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.190 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7P4C

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

1,6- epi-Cyclophellitol Cyclosulfamidate Is a Bona Fide Lysosomal alpha-Glucosidase Stabilizer for the Treatment of Pompe Disease.

Kok, K.Kuo, C.L.Katzy, R.E.Lelieveld, L.T.Wu, L.Roig-Zamboni, V.van der Marel, G.A.Codee, J.D.C.Sulzenbacher, G.Davies, G.J.Overkleeft, H.S.Aerts, J.M.F.G.Artola, M.

(2022) J Am Chem Soc 144: 14819-14827

  • DOI: https://doi.org/10.1021/jacs.2c05666
  • Primary Citation Related Structures: 
    7P2Z, 7P32, 7P4C, 7P4D

  • PubMed Abstract: 

    α-Glucosidase inhibitors are potential therapeutics for the treatment of diabetes, viral infections, and Pompe disease. Herein, we report a 1,6- epi -cyclophellitol cyclosulfamidate as a new class of reversible α-glucosidase inhibitors that displays enzyme inhibitory activity by virtue of its conformational mimicry of the substrate when bound in the Michaelis complex. The α-d- glc- configured cyclophellitol cyclosulfamidate 4 binds in a competitive manner the human lysosomal acid α-glucosidase (GAA), ER α-glucosidases, and, at higher concentrations, intestinal α-glucosidases, displaying an excellent selectivity over the human β-glucosidases GBA and GBA2 and glucosylceramide synthase (GCS). Cyclosulfamidate 4 stabilizes recombinant human GAA (rhGAA, alglucosidase alfa, Myozyme) in cell medium and plasma and facilitates enzyme trafficking to lysosomes. It stabilizes rhGAA more effectively than existing small-molecule chaperones and does so in vitro , in cellulo , and in vivo in zebrafish, thus representing a promising therapeutic alternative to Miglustat for Pompe disease.


  • Organizational Affiliation
    • Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 96.05 kDa 
  • Atom Count: 6,789 
  • Modeled Residue Count: 780 
  • Deposited Residue Count: 836 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Oligosaccharide 4-alpha-D-glucosyltransferaseA [auth AAA]836Cellvibrio 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
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5OV
(Subject of Investigation/LOI)

Query on 5OV



Download:Ideal Coordinates CCD File
F [auth AAA](3aR,4S,5S,6R,7R,7aS)-7-(hydroxymethyl)-2,2-bis(oxidanylidene)-3a,4,5,6,7,7a-hexahydro-3H-benzo[d][1,2,3]oxathiazole-4,5,6-triol
C7 H13 N O7 S
LDXSPHJOJCEWFB-MAFUWASYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
H [auth AAA]
I [auth AAA]
J [auth AAA]
K [auth AAA]
L [auth AAA]
H [auth AAA],
I [auth AAA],
J [auth AAA],
K [auth AAA],
L [auth AAA],
M [auth AAA],
N [auth AAA],
O [auth AAA],
P [auth AAA]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
OXL

Query on OXL



Download:Ideal Coordinates CCD File
D [auth AAA]OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
B [auth AAA],
C [auth AAA],
E [auth AAA],
G [auth AAA]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free:  0.229 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
Space Group: P 6 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 197α = 90
b = 197β = 90
c = 102.156γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)United KingdomAdG-322942

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-27
    Type: Initial release
  • Version 1.1: 2022-08-31
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary