8P3E

Crystal structure of glucocerebrosidase in complex with allosteric activator

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

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This is version 1.2 of the entry. See complete history. 


Literature

Identification of ss-Glucocerebrosidase Activators for Glucosylceramide hydrolysis.

Schulze, M.E.D., Scholz, D., Jnoff, E., Hall, A., Melin, J., Sands, Z.A., Rodriguez, E., Andre, V.M.

(2024) ChemMedChem 19: e202300548-e202300548

  • DOI: https://doi.org/10.1002/cmdc.202300548
  • Primary Citation of Related Structures:  
    8P3E, 8P41

  • PubMed Abstract: 

    Several novel chemical series were identified that modulate glucocerebrosidase (GCase). Compounds from these series are active on glucosylceramide, unlike other known GCase modulators. We obtained GCase crystal structures with two compounds that have distinct chemotypes. Positive allosteric modulators bind to a site on GCase and induce conformational changes, but also induce an equilibrium state between monomer and dimer.

    • Organizational Affiliation: 

    UCB, 216 Bath Road, Slough, SL1 3WE, UK.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucosylceramidase
A, B
497Homo sapiensMutation(s): 0 
Gene Names: GBA, GC, GLUC
EC: 3.2.1.45 (PDB Primary Data), 2.4.1 (PDB Primary Data), 3.2.1.104 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P04062 (Homo sapiens)
Explore P04062 
Go to UniProtKB:  P04062
PHAROS:  P04062
GTEx:  ENSG00000177628 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04062
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WSI (Subject of Investigation/LOI)
Query on WSI
Download Ideal Coordinates CCD File 
F [auth B]2-[[3-[(4-chlorophenyl)carbamoyl]phenyl]sulfonylamino]benzoic acid
C20 H15 Cl N2 O5 S
VFTDTUYAXCTQQQ-UHFFFAOYSA-N
NAG
Query on NAG
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.31α = 90
b = 285.64β = 90
c = 91.87γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release
  • Version 1.1: 2024-04-24
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Database references