7P32 | pdb_00007p32

Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with cyclosulfamidate 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 
    0.175 (Depositor), 0.188 (DCC) 
  • R-Value Work: 
    0.150 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 
    0.151 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7P32

Ligand Structure Quality Assessment 


This is version 2.1 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: 100.88 kDa 
  • Atom Count: 7,681 
  • Modeled Residue Count: 847 
  • Deposited Residue Count: 872 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lysosomal alpha-glucosidaseA [auth AAA]872Homo sapiensMutation(s): 3 
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

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth BBB]3N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB
GlyCosmos: G21290RB
GlyGen: G21290RB
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth BcB]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth BfB]3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth BiB]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G86851RC
GlyCosmos: G86851RC
GlyGen: G86851RC

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
56I
(Subject of Investigation/LOI)

Query on 56I



Download:Ideal Coordinates CCD File
G [auth AAA][(1R,2R,3R,4R,5S)-2-(hydroxymethyl)-3,4,5-tris(oxidanyl)cyclohexyl]sulfamic acid
C7 H15 N O7 S
QOECHHYORUOADE-PJEQPVAWSA-N
NAG
(Subject of Investigation/LOI)

Query on NAG



Download:Ideal Coordinates CCD File
F [auth AAA]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PGE
(Subject of Investigation/LOI)

Query on PGE



Download:Ideal Coordinates CCD File
CA [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],
I [auth AAA],
J [auth AAA],
K [auth AAA],
L [auth AAA]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
(Subject of Investigation/LOI)

Query on GOL



Download:Ideal Coordinates CCD File
V [auth AAA],
W [auth AAA],
X [auth AAA]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
(Subject of Investigation/LOI)

Query on EDO



Download:Ideal Coordinates CCD File
AA [auth AAA],
BA [auth AAA],
Y [auth AAA],
Z [auth AAA]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
(Subject of Investigation/LOI)

Query on CL



Download:Ideal Coordinates CCD File
M [auth AAA]
N [auth AAA]
O [auth AAA]
P [auth AAA]
Q [auth AAA]
M [auth AAA],
N [auth AAA],
O [auth AAA],
P [auth AAA],
Q [auth AAA],
R [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]L-PEPTIDE LINKINGC3 H7 N O3 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free:  0.175 (Depositor), 0.188 (DCC) 
  • R-Value Work:  0.150 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 0.151 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.043α = 90
b = 102.606β = 90
c = 129.118γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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 2.0: 2024-07-31
    Changes: Atomic model, Data collection, Source and taxonomy, Structure summary
  • Version 2.1: 2024-11-13
    Changes: Structure summary