7KHV

CpOGA IN COMPLEX WITH LIGAND 54


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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 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
A, B, C, D, E, F
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]
FA [auth D],
G [auth A],
O [auth B],
QA [auth E],
W [auth C],
WA [auth F]
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]
AA [auth C],
AB [auth F],
BA [auth C],
BB [auth F],
CA [auth C],
CB [auth F],
DA [auth C],
EA [auth C],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
KA [auth D],
L [auth A],
LA [auth D],
M [auth A],
MA [auth D],
N [auth A],
NA [auth D],
OA [auth D],
PA [auth D],
R [auth B],
S [auth B],
SA [auth E],
T [auth B],
TA [auth E],
U [auth B],
UA [auth E],
V [auth B],
VA [auth E],
Y [auth C],
YA [auth F],
Z [auth C],
ZA [auth F]
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 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • 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

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