6TBJ

Structure of a beta galactosidase with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Mechanistic Insights into the Chaperoning of Human Lysosomal-Galactosidase Activity: Highly Functionalized Aminocyclopentanes and C -5a-Substituted Derivatives of 4- epi -Isofagomine.

Weber, P.Thonhofer, M.Averill, S.Davies, G.J.Santana, A.G.Muller, P.Nasseri, S.A.Offen, W.A.Pabst, B.M.Paschke, E.Schalli, M.Torvisco, A.Tschernutter, M.Tysoe, C.Windischhofer, W.Withers, S.G.Wolfsgruber, A.Wrodnigg, T.M.Stutz, A.E.

(2020) Molecules 25

  • DOI: https://doi.org/10.3390/molecules25174025
  • Primary Citation of Related Structures:  
    6TBF, 6TBG, 6TBH, 6TBI, 6TBJ, 6TBK

  • PubMed Abstract: 

    Glycosidase inhibitors have shown great potential as pharmacological chaperones for lysosomal storage diseases. In light of this, a series of new cyclopentanoid β-galactosidase inhibitors were prepared and their inhibitory and pharmacological chaperoning activities determined and compared with those of lipophilic analogs of the potent β-d-galactosidase inhibitor 4- epi -isofagomine. Structure-activity relationships were investigated by X-ray crystallography as well as by alterations in the cyclopentane moiety such as deoxygenation and replacement by fluorine of a "strategic" hydroxyl group. New compounds have revealed highly promising activities with a range of β-galactosidase-compromised human cell lines and may serve as leads towards new pharmacological chaperones for G M1 -gangliosidosis and Morquio B disease.


  • Organizational Affiliation

    Glycogroup, Institute of Chemistry and Technology of Biobased Systems, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-galactosidase, putative, bgl35A
A, B, C, D, E
A, B, C, D, E, F, G, H
550Cellvibrio japonicus Ueda107Mutation(s): 0 
Gene Names: bgl35ACJA_2707
EC: 3.2.1.23
UniProt
Find proteins for B3PBE0 (Cellvibrio japonicus (strain Ueda107))
Explore B3PBE0 
Go to UniProtKB:  B3PBE0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3PBE0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N0W (Subject of Investigation/LOI)
Query on N0W

Download Ideal Coordinates CCD File 
CA [auth E]
HA [auth F]
L [auth A]
LA [auth G]
N [auth B]
CA [auth E],
HA [auth F],
L [auth A],
LA [auth G],
N [auth B],
QA [auth H],
R [auth C],
X [auth D]
5-(dimethylamino)-~{N}-[6-[(2~{S},3~{R},4~{S},5~{R})-3-(hydroxymethyl)-4,5-bis(oxidanyl)piperidin-2-yl]hexyl]naphthalene-1-sulfonamide
C24 H37 N3 O5 S
YUUSOYGEJQMOTK-QRVLJTFESA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
DA [auth F]
EA [auth F]
FA [auth F]
AA [auth E],
BA [auth E],
DA [auth F],
EA [auth F],
FA [auth F],
GA [auth F],
I [auth A],
IA [auth G],
J [auth A],
JA [auth G],
K [auth A],
KA [auth G],
M [auth B],
MA [auth H],
NA [auth H],
O [auth C],
OA [auth H],
P [auth C],
PA [auth H],
Q [auth C],
S [auth D],
T [auth D],
U [auth D],
V [auth D],
W [auth D],
Y [auth E],
Z [auth E]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.416α = 89.93
b = 115.786β = 90.08
c = 116.186γ = 89.99
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/R001162/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2021-03-03
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description