7P2Z

Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with cyclosulfamidate 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.175 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.148 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.150 (Depositor) 

Starting Model: experimental
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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 YTWClick on this verticalbar to view detailsBest fitted PGEClick on this verticalbar to view detailsBest fitted SO4Click on this verticalbar to view detailsBest fitted GOLClick on this verticalbar to view detailsBest fitted EDOClick on this verticalbar to view details

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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysosomal alpha-glucosidaseA [auth AAA],
B [auth AaA]
872Homo sapiensMutation(s): 0 
Gene Names: GAA
EC: 3.2.1.20
UniProt & NIH Common Fund Data Resources
Find proteins for P10253 (Homo sapiens)
Explore P10253 
Go to UniProtKB:  P10253
PHAROS:  P10253
GTEx:  ENSG00000171298 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10253
Glycosylation
Glycosylation Sites: 5Go to GlyGen: P10253-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth BBB]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth BcB],
E [auth BeB]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth BgB]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth BjB]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YTW (Subject of Investigation/LOI)
Query on YTW

Download Ideal Coordinates CCD File 
N [auth AaA](3~{a}~{R},4~{S},5~{S},6~{S},7~{R},7~{a}~{S})-7-(hydroxymethyl)-2,2-bis(oxidanylidene)-3~{a},4,5,6,7,7~{a}-hexahydro-3~{H}-benzo[d][1,2,3]oxathiazole-4,5,6-triol
C7 H13 N O7 S
LDXSPHJOJCEWFB-MREPKMFUSA-N
PGE (Subject of Investigation/LOI)
Query on PGE

Download Ideal Coordinates CCD File 
EA [auth AaA],
FA [auth AaA]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
H [auth AAA],
O [auth AaA],
P [auth AaA],
Q [auth AaA],
R [auth AaA]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth AaA],
K [auth AAA],
Z [auth AaA]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth AaA],
CA [auth AaA],
DA [auth AaA],
L [auth AAA],
M [auth AaA]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
I [auth AAA]
J [auth AAA]
S [auth AaA]
T [auth AaA]
U [auth AaA]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A [auth AAA],
B [auth AaA]
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.175 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.148 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.150 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.157α = 90
b = 102.539β = 90
c = 129.048γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

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 YTWClick on this verticalbar to view detailsBest fitted PGEClick on this verticalbar to view detailsBest fitted SO4Click on this verticalbar to view detailsBest fitted GOLClick on this verticalbar to view detailsBest fitted EDOClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    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