7KHV

CpOGA IN COMPLEX WITH LIGAND 54


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.247 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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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 X1AClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Diazaspirononane Nonsaccharide Inhibitors of O-GlcNAcase (OGA) for the Treatment of Neurodegenerative Disorders.

Martinez-Viturro, C.M.Trabanco, A.A.Royes, J.Fernandez, E.Tresadern, G.Vega, J.A.Del Cerro, A.Delgado, F.Garcia Molina, A.Tovar, F.Shaffer, P.Ebneth, A.Bretteville, A.Mertens, L.Somers, M.Alonso, J.M.Bartolome-Nebreda, J.M.

(2020) J Med Chem 63: 14017-14044

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01479
  • Primary Citation of Related Structures:  
    7KHS, 7KHV

  • PubMed Abstract: 

    O-GlcNAcylation is a post-translational modification of tau understood to lower the speed and yield of its aggregation, a pathological hallmark of Alzheimer's disease (AD). O-GlcNAcase (OGA) is the only enzyme that removes O-linked N -acetyl-d-glucosamine (O-GlcNAc) from target proteins. Therefore, inhibition of OGA represents a potential approach for the treatment of AD by preserving the O-GlcNAcylated tau protein. Herein, we report the multifactorial optimization of high-throughput screening hit 8 to a potent, metabolically stable, and orally bioavailable diazaspirononane OGA inhibitor (+)- 56 . The human OGA X-ray crystal structure has been recently solved, but bacterial hydrolases are still widely used as structural homologues. For the first time, we reveal how a nonsaccharide series of inhibitors binds bacterial OGA and discuss the suitability of two different bacterial orthologues as surrogates for human OGA. These breakthroughs enabled structure-activity relationships to be understood and provided context and boundaries for the optimization of druglike properties.


  • Organizational Affiliation

    Discovery Chemistry, Janssen Research & Development, Janssen-Cilag S.A., C/Jarama 75A, 45007 Toledo, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
O-GlcNAcase NagJ
A, B, C, D, E
594Clostridium perfringensMutation(s): 3 
Gene Names: nagJCPF_1442
EC: 3.2.1.169
UniProt
Find proteins for Q0TR53 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A))
Explore Q0TR53 
Go to UniProtKB:  Q0TR53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0TR53
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X1A
Query on X1A

Download Ideal Coordinates CCD File 
FA [auth D]
G [auth A]
O [auth B]
QA [auth E]
W [auth C]
N-(5-{[6-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)-2,6-diazaspiro[3.4]octan-2-yl]methyl}-1,3-thiazol-2-yl)acetamide
C18 H22 N8 O S
DSEWUBFXIVTHKH-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C]
AB [auth F]
BA [auth C]
BB [auth F]
CA [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA
Query on CA

Download Ideal Coordinates CCD File 
GA [auth D],
H [auth A],
RA [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
HA [auth D],
P [auth B],
Q [auth B],
X [auth C],
XA [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.489α = 90
b = 178.104β = 90
c = 407.054γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

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 X1AClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Advisory, Data collection, Database references
  • Version 1.2: 2024-04-03
    Changes: Refinement description