9FAY

Gcase in complex with small molecule inhibitor 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.183 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.148 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.150 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1IBRClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Fragment-Based Discovery of a Series of Allosteric-Binding Site Modulators of beta-Glucocerebrosidase.

Palmer, N.Agnew, C.Benn, C.Buffham, W.J.Castro, J.N.Chessari, G.Clark, M.Cons, B.D.Coyle, J.E.Dawson, L.A.Hamlett, C.C.F.Hodson, C.Holding, F.Johnson, C.N.Liebeschuetz, J.W.Mahajan, P.McCarthy, J.M.Murray, C.W.O'Reilly, M.Peakman, T.Price, A.Rapti, M.Reeks, J.Schopf, P.St-Denis, J.D.Valenzano, C.Wallis, N.G.Walser, R.Weir, H.Wilsher, N.E.Woodhead, A.Bento, C.F.Tisi, D.

(2024) J Med Chem 67: 11168-11181

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00702
  • Primary Citation of Related Structures:  
    9F9Z, 9FA3, 9FA6, 9FAD, 9FAL, 9FAY, 9FAZ, 9FB2, 9FDI

  • PubMed Abstract: 

    β-Glucocerebrosidase (GBA/GCase) mutations leading to misfolded protein cause Gaucher's disease and are a major genetic risk factor for Parkinson's disease and dementia with Lewy bodies. The identification of small molecule pharmacological chaperones that can stabilize the misfolded protein and increase delivery of degradation-prone mutant GCase to the lysosome is a strategy under active investigation. Here, we describe the first use of fragment-based drug discovery (FBDD) to identify pharmacological chaperones of GCase. The fragment hits were identified by using X-ray crystallography and biophysical techniques. This work led to the discovery of a series of compounds that bind GCase with nM potency and positively modulate GCase activity in cells.


  • Organizational Affiliation

    Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysosomal acid glucosylceramidase546Homo sapiensMutation(s): 0 
Gene Names: GBA1GBAGCGLUC
EC: 3.2.1.45 (PDB Primary Data), 2.4.1 (PDB Primary Data), 3.2.1 (PDB Primary Data), 3.2.1.46 (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
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P04062-1
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
B, C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IBR (Subject of Investigation/LOI)
Query on A1IBR

Download Ideal Coordinates CCD File 
L [auth A]~{N}-[(2~{S})-2-azanyl-2-phenyl-ethyl]-3,5-bis(fluoranyl)-~{N}-methyl-benzenesulfonamide
C15 H16 F2 N2 O2 S
FNCHZOWWNSAAOH-OAHLLOKOSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
G [auth A],
J [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
K [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.183 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.148 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.150 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.878α = 90
b = 74.481β = 102.63
c = 68.359γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1IBRClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-03
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Database references
  • Version 1.2: 2024-10-09
    Changes: Structure summary