9FA6 | pdb_00009fa6

Gcase in complex with small molecule inhibitor 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 
    0.232 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 9FA6

Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 63.15 kDa 
  • Atom Count: 4,580 
  • Modeled Residue Count: 501 
  • Deposited Residue Count: 546 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 GlycosylationD 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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IBG
(Subject of Investigation/LOI)

Query on A1IBG



Download:Ideal Coordinates CCD File
I [auth A]~{N}-[(2~{R})-3-azanyl-2-oxidanyl-propyl]-2-fluoranyl-benzenesulfonamide
C9 H13 F N2 O3 S
XRJZVFBXOJFVLU-SSDOTTSWSA-N
A1IBE
(Subject of Investigation/LOI)

Query on A1IBE



Download:Ideal Coordinates CCD File
H [auth A],
J [auth A]
~{N}-[(2~{S})-3-azanyl-2-oxidanyl-propyl]-2-fluoranyl-benzenesulfonamide
C9 H13 F N2 O3 S
XRJZVFBXOJFVLU-ZETCQYMHSA-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
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
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: 1.49 Å
  • R-Value Free:  0.232 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.689α = 90
b = 74.025β = 102.64
c = 68.701γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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: 2024-10-16
    Changes: Structure summary