7KHS | pdb_00007khs

OgOGA IN COMPLEX WITH LIGAND 55


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.296 (Depositor), 0.295 (DCC) 
  • R-Value Work: 
    0.273 (Depositor), 0.272 (DCC) 
  • R-Value Observed: 
    0.273 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 202.76 kDa 
  • Atom Count: 14,318 
  • Modeled Residue Count: 1,754 
  • Deposited Residue Count: 1,796 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein O-GlcNAcase
A, B, C, D
449Oceanicola granulosus HTCC2516Mutation(s): 0 
Gene Names: OG2516_04129
EC: 3.2.1.169
UniProt
Find proteins for Q2CEE3 (Oceanicola granulosus (strain ATCC BAA-861 / DSM 15982 / KCTC 12143 / HTCC2516))
Explore Q2CEE3 
Go to UniProtKB:  Q2CEE3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2CEE3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WG4
(Subject of Investigation/LOI)

Query on WG4



Download:Ideal Coordinates CCD File
E [auth A],
F [auth B],
H [auth C],
J [auth D]
N-(5-{[(5S)-7-(5-methylimidazo[1,2-a]pyrimidin-7-yl)-2,7-diazaspiro[4.4]nonan-2-yl]methyl}-1,3-thiazol-2-yl)acetamide
C20 H25 N7 O S
RJDUUKXZMXIWIE-FQEVSTJZSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
I [auth C]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
G [auth B],
K [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.296 (Depositor), 0.295 (DCC) 
  • R-Value Work:  0.273 (Depositor), 0.272 (DCC) 
  • R-Value Observed: 0.273 (Depositor) 
Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.231α = 90
b = 83.076β = 90.25
c = 122.964γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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, Refinement description
  • Version 1.2: 2024-04-03
    Changes: Refinement description