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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Ligand Structure Quality Assessment 


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: https://doi.org/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. 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

    Pharmaron Beijing Co. Ltd. , 6 Taihe Road, BDA , Beijing 100176 , P. R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
O-GlcNAcase TIM-barrel domain
A, B, C, D
388Homo sapiensMutation(s): 0 
Gene Names: MGEA5HEXCKIAA0679MEA5
EC: 3.2.1.169
UniProt & NIH Common Fund Data Resources
Find proteins for O60502 (Homo sapiens)
Explore O60502 
Go to UniProtKB:  O60502
GTEx:  ENSG00000198408 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60502
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
O-GlcNAcase stalk domain
E, F, G, H
161Homo sapiensMutation(s): 0 
Gene Names: MGEA5HEXCKIAA0679MEA5
EC: 3.2.1.169
UniProt & NIH Common Fund Data Resources
Find proteins for O60502 (Homo sapiens)
Explore O60502 
Go to UniProtKB:  O60502
GTEx:  ENSG00000198408 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60502
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
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