3RIK

The acid beta-glucosidase active site exhibits plasticity in binding 3,4,5,6-tetrahydroxyazepane-based inhibitors: implications for pharmacological chaperone design for gaucher disease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Binding of 3,4,5,6-tetrahydroxyazepanes to the acid-beta-glucosidase active site: implications for pharmacological chaperone design for Gaucher disease

Orwig, S.D.Tan, Y.L.Grimster, N.P.Yu, Z.Powers, E.T.Kelly, J.W.Lieberman, R.L.

(2011) Biochemistry 50: 10647-10657

  • DOI: 10.1021/bi201619z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pharmacologic chaperoning is a therapeutic strategy being developed to improve the cellular folding and trafficking defects associated with Gaucher disease, a lysosomal storage disorder caused by point mutations in the gene encoding acid-β-glucosidas ...

    Pharmacologic chaperoning is a therapeutic strategy being developed to improve the cellular folding and trafficking defects associated with Gaucher disease, a lysosomal storage disorder caused by point mutations in the gene encoding acid-β-glucosidase (GCase). In this approach, small molecules bind to and stabilize mutant folded or nearly folded GCase in the endoplasmic reticulum (ER), increasing the concentration of folded, functional GCase trafficked to the lysosome where the mutant enzyme can hydrolyze the accumulated substrate. To date, the pharmacologic chaperone (PC) candidates that have been investigated largely have been active site-directed inhibitors of GCase, usually containing five- or six-membered rings, such as modified azasugars. Here we show that a seven-membered, nitrogen-containing heterocycle (3,4,5,6-tetrahydroxyazepane) scaffold is also promising for generating PCs for GCase. Crystal structures reveal that the core azepane stabilizes GCase in a variation of its proposed active conformation, whereas binding of an analogue with an N-linked hydroxyethyl tail stabilizes GCase in a conformation in which the active site is covered, also utilizing a loop conformation not seen previously. Although both compounds preferentially stabilize GCase to thermal denaturation at pH 7.4, reflective of the pH in the ER, only the core azepane, which is a mid-micromolar competitive inhibitor, elicits a modest increase in enzyme activity for the neuronopathic G202R and the non-neuronopathic N370S mutant GCase in an intact cell assay. Our results emphasize the importance of the conformational variability of the GCase active site in the design of competitive inhibitors as PCs for Gaucher disease.


    Organizational Affiliation

    School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucosylceramidase
A, B, C, D
497Homo sapiensMutation(s): 0 
Gene Names: GBA (GC, GLUC)
EC: 3.2.1.45
Find proteins for P04062 (Homo sapiens)
Go to Gene View: GBA
Go to UniProtKB:  P04062
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
3RI
Query on 3RI

Download SDF File 
Download CCD File 
B, D
(3S,4R,5R,6S)-1-(2-hydroxyethyl)azepane-3,4,5,6-tetrol
C8 H17 N O5
VWGJHYNWDXVPIU-RULNZFCNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3RIIC50: 3400000 nM BINDINGMOAD
3RIIC50: 3400000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 107.980α = 90.00
b = 91.553β = 110.70
c = 152.213γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACphasing
HKL-2000data scaling
REFMACrefinement
SERGUIdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2012-12-05
    Type: Derived calculations
  • Version 1.2: 2018-08-15
    Type: Advisory, Data collection, Derived calculations