9GTN | pdb_00009gtn

Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with iminosugar compound 4k


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.177 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.152 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.153 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9GTN

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

C -Branched Iminosugars as Selective Pharmacological Chaperones of Lysosomal alpha-Glucosidase for the Treatment of Pompe Disease.

Vieira Da Cruz, A.Perraudin, V.Minopoli, N.Iacono, R.Roig-Zamboni, V.Bossio, A.Tangara, S.Fayolle, M.Kanazawa, A.Philouze, C.Tarallo, A.Heming, J.J.A.Artola, M.Behr, J.B.Overkleeft, H.S.Moracci, M.Sulzenbacher, G.Parenti, G.Py, S.

(2025) J Med Chem 68: 19269-19286

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01349
  • Primary Citation Related Structures: 
    9GSV, 9GSW, 9GTC, 9GTD, 9GTL, 9GTN, 9GTT, 9GTW

  • PubMed Abstract: 

    We report herein the design and synthesis of a series of 5- C -alkyldeoxynojirimycins from l-sorbose, through an efficient and scalable method amenable to preparing a large variety of analogues. The interaction of this class of compounds with human acid α-glucosidase (GAA), the genetically defective enzyme in patients suffering from Pompe disease, was investigated to identify pharmacological chaperones exhibiting high selectivity for this enzyme. Crystallographic analyses provided a rationale for their binding mode to GAA and chaperone activity. The effects of 5- C -phenethyl-DNJ ( 4c ) were evaluated on GAA activity enhancement in cells from Pompe disease patients and in vivo in GAA-KO mice. The significant increase of GAA activity in the presence of 4c in various tissues, particularly in the diaphragm, encourages further studies on this class of small molecules toward developing clinical drugs. Their chaperone activity and excellent selectivity may offer potential benefits over the current treatments for Pompe disease.


  • Organizational Affiliation
    • Université Grenoble Alpes, CNRS, DCM, 38000 Grenoble, France.

Macromolecule Content 

  • Total Structure Weight: 110.37 kDa 
  • Atom Count: 7,806 
  • Modeled Residue Count: 860 
  • Deposited Residue Count: 952 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lysosomal alpha-glucosidase952Homo 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

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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-glucopyranose
B, F
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-glucopyranose
C, D
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-glucopyranose
E
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IPA

Query on A1IPA



Download:Ideal Coordinates CCD File
H [auth A](2~{R},3~{R},4~{R},5~{S})-2-(2-hydroxyethyl)-2-(hydroxymethyl)piperidine-3,4,5-triol
C8 H17 N O5
UKHJGUGGTKLIIF-FKSUSPILSA-N
PGE
(Subject of Investigation/LOI)

Query on PGE



Download:Ideal Coordinates CCD File
BA [auth A],
CA [auth A],
IA [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
EA [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
K [auth A],
L [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
AA [auth A],
FA [auth A],
GA [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
DA [auth A]
G [auth A]
HA [auth A]
R [auth A]
S [auth A]
DA [auth A],
G [auth A],
HA [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.177 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.152 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.677α = 90
b = 102.385β = 90
c = 128.063γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-01
    Type: Initial release
  • Version 1.1: 2025-10-08
    Changes: Database references