8R06

CRYSTAL STRUCTURE OF THERMOANAEROBACTERIUM XYLANOLYTICUM GH116 BETA-GLUCOSIDASE WITH A COVALENTLY BOUND CYCLOPHELLITOL AZIRIDINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 5NCX


Literature

CRYSTAL STRUCTURE OF THERMOANAEROBACTERIUM XYLOLYTICUM GH116 BETA-GLUCOSIDASE WITH A COVALENTLY BOUND CYCLOPHELLITOL AZIRIDINE

Lahav, D.Liu, B.van den Berg, R.J.B.H.N.van den Nieuwendijk, A.M.C.H.Wennekes, T.Ghisaidoobe, A.T.Breen, I.Ferraz, M.J.Kuo, C.-L.Wu, L.Geurink, P.P.Ovaa, H.van der Marel, G.A.van der Stelt, M.Boot, R.G.Davies, G.J.Aerts, J.M.F.G.Overkleeft, H.S.

(2017) J Am Chem Soc 40: 14192-14197

  • DOI: https://doi.org/10.1021/jacs.7b07352
  • Primary Citation of Related Structures:  
    8R06

  • PubMed Abstract: 

    Human nonlysosomal glucosylceramidase (GBA2) is one of several enzymes that controls levels of glycolipids and whose activity is linked to several human disease states. There is a major need to design or discover selective GBA2 inhibitors both as chemical tools and as potential therapeutic agents. Here, we describe the development of a fluorescence polarization activity-based protein profiling (FluoPol-ABPP) assay for the rapid identification, from a 350+ library of iminosugars, of GBA2 inhibitors. A focused library is generated based on leads from the FluoPol-ABPP screen and assessed on GBA2 selectivity offset against the other glucosylceramide metabolizing enzymes, glucosylceramide synthase (GCS), lysosomal glucosylceramidase (GBA), and the cytosolic retaining β-glucosidase, GBA3. Our work, yielding potent and selective GBA2 inhibitors, also provides a roadmap for the development of high-throughput assays for identifying retaining glycosidase inhibitors by FluoPol-ABPP on cell extracts containing recombinant, overexpressed glycosidase as the easily accessible enzyme source.


  • Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, The University of York , York YO10 5DD, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucosylceramidase799Thermoanaerobacterium xylanolyticum LX-11Mutation(s): 0 
Gene Names: Thexy_2211
EC: 3.2.1.45
UniProt
Find proteins for F6BL85 (Thermoanaerobacterium xylanolyticum (strain ATCC 49914 / DSM 7097 / LX-11))
Explore F6BL85 
Go to UniProtKB:  F6BL85
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF6BL85
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO8 (Subject of Investigation/LOI)
Query on PO8

Download Ideal Coordinates CCD File 
B [auth A](1~{R},2~{S},3~{S},4~{S},5~{R},6~{R})-5-azanyl-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol
C7 H16 N O5
SWVTZDDSAFUTKS-ARYBSUEZSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.621α = 90
b = 83.295β = 90
c = 177.48γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European UnionERC-2012-AdG-322942

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary