6TBF

Structure of a beta galactosidase with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.130 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N0T (Subject of Investigation/LOI)
Query on N0T

Download Ideal Coordinates CCD File 
BA [auth D]
HB [auth H]
J [auth A]
JA [auth E]
P [auth B]
BA [auth D],
HB [auth H],
J [auth A],
JA [auth E],
P [auth B],
SA [auth F],
U [auth C],
YA [auth G]
(1~{S},2~{S},3~{S},4~{R},5~{R})-4-(hydroxymethyl)-5-(octylamino)cyclopentane-1,2,3-triol
C14 H29 N O4
UZTOTQLQFAGSAI-NDKCEZKHSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AA [auth D]
AB [auth G]
BB [auth G]
CA [auth D]
CB [auth G]
AA [auth D],
AB [auth G],
BB [auth G],
CA [auth D],
CB [auth G],
DA [auth D],
IB [auth H],
K [auth A],
KA [auth E],
LA [auth E],
Q [auth B],
TA [auth F],
UA [auth F],
ZA [auth G]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
DB [auth G]
EA [auth D]
EB [auth G]
FA [auth D]
FB [auth G]
DB [auth G],
EA [auth D],
EB [auth G],
FA [auth D],
FB [auth G],
GA [auth E],
GB [auth H],
HA [auth E],
I [auth A],
IA [auth E],
JB [auth H],
KB [auth H],
L [auth A],
LB [auth H],
M [auth A],
MA [auth E],
MB [auth H],
N [auth A],
NA [auth E],
O [auth B],
OA [auth E],
PA [auth F],
QA [auth F],
R [auth B],
RA [auth F],
S [auth C],
T [auth C],
V [auth C],
VA [auth F],
W [auth C],
WA [auth G],
X [auth D],
XA [auth G],
Y [auth D],
Z [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.130 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.423α = 90.35
b = 115.626β = 90.02
c = 115.942γ = 90.16
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
Aimlessdata scaling
REFMACphasing

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: 2022-03-02
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Refinement description