6PM9

Crystal structure of the core catalytic domain of human O-GlcNAcase bound to MK-8719


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.243 

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This is version 1.1 of the entry. See complete history


Literature

Discovery of MK-8719, a Potent O-GlcNAcase Inhibitor as a Potential Treatment for Tauopathies.

Selnick, H.G.Hess, J.F.Tang, C.Liu, K.Schachter, J.B.Ballard, J.E.Marcus, J.Klein, D.J.Wang, X.Pearson, M.Savage, M.J.Kaul, R.Li, T.S.Vocadlo, D.J.Zhou, Y.Zhu, Y.Mu, C.Wang, Y.Wei, Z.Bai, C.Duffy, J.L.McEachern, E.J.

(2019) J Med Chem 62: 10062-10097

  • DOI: 10.1021/acs.jmedchem.9b01090
  • Primary Citation of Related Structures:  
    6PM9

  • PubMed Abstract: 
  • Inhibition of O-GlcNAcase (OGA) has emerged as a promising therapeutic approach to treat tau pathology in neurodegenerative diseases such as Alzheimer's disease and progressive supranuclear palsy. Beginning with carbohydrate-based lead molecules, we pursued an optimization strategy of reducing polar surface area to align the desired drug-like properties of potency, selectivity, high central nervous system (CNS) exposure, metabolic stability, favorable pharmacokinetics, and robust in vivo pharmacodynamic response ...

    Inhibition of O-GlcNAcase (OGA) has emerged as a promising therapeutic approach to treat tau pathology in neurodegenerative diseases such as Alzheimer's disease and progressive supranuclear palsy. Beginning with carbohydrate-based lead molecules, we pursued an optimization strategy of reducing polar surface area to align the desired drug-like properties of potency, selectivity, high central nervous system (CNS) exposure, metabolic stability, favorable pharmacokinetics, and robust in vivo pharmacodynamic response. Herein, we describe the medicinal chemistry and pharmacological studies that led to the identification of (3a R ,5 S ,6 S ,7 R ,7a R )-5-(difluoromethyl)-2-(ethylamino)-3a,6,7,7a-tetrahydro-5 H -pyrano[3,2- d ]thiazole-6,7-diol 42 (MK-8719), a highly potent and selective OGA inhibitor with excellent CNS penetration that has been advanced to first-in-human phase I clinical trials.


    Organizational Affiliation

    Alectos Therapeutics Inc. , 8999 Nelson Way , Burnaby , British Columbia V5A 4B5 , Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
O-GlcNAcase TIM-barrel domainA, B, C, D388Homo sapiensMutation(s): 0 
Gene Names: MGEA5HEXCKIAA0679MEA5OGA
EC: 3.2.1.169
UniProt & NIH Common Fund Data Resources
Find proteins for O60502 (Homo sapiens)
Explore O60502 
Go to UniProtKB:  O60502
PHAROS:  O60502
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
O-GlcNAcase stalk domainE, F, G, H161Homo sapiensMutation(s): 0 
Gene Names: MGEA5HEXCKIAA0679MEA5OGA
EC: 3.2.1.169
UniProt & NIH Common Fund Data Resources
Find proteins for O60502 (Homo sapiens)
Explore O60502 
Go to UniProtKB:  O60502
PHAROS:  O60502
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OQ1 (Subject of Investigation/LOI)
Query on OQ1

Download Ideal Coordinates CCD File 
I [auth A], J [auth B], K [auth C], L [auth D](3aR,5S,6S,7R,7aR)-5-(difluoromethyl)-2-(ethylamino)-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol
C9 H14 F2 N2 O3 S
UDQTXCHQKHIQMH-KYGLGHNPSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
OQ1 BindingDB:  6PM9 Ki: min: 5.7, max: 7.9 (nM) from 2 assay(s)
IC50: 7.9 (nM) from 1 assay(s)
EC50: min: 53, max: 53 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.243 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.92α = 77.27
b = 91.46β = 62.61
c = 94.61γ = 62.86
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Database references