BACE1 in complex with 4-(3-(furan-2-carboxamido)phenyl)-1-methyl-5-oxo-4-phenylimidazolidin-2-iminium

Experimental Data Snapshot

  • Resolution: 1.83 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

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This is version 1.2 of the entry. See complete history


Discovery of the 3-Imino-1,2,4-thiadiazinane 1,1-Dioxide Derivative Verubecestat (MK-8931)-A beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 Inhibitor for the Treatment of Alzheimer's Disease.

Scott, J.D.Li, S.W.Brunskill, A.P.Chen, X.Cox, K.Cumming, J.N.Forman, M.Gilbert, E.J.Hodgson, R.A.Hyde, L.A.Jiang, Q.Iserloh, U.Kazakevich, I.Kuvelkar, R.Mei, H.Meredith, J.Misiaszek, J.Orth, P.Rossiter, L.M.Slater, M.Stone, J.Strickland, C.O.Voigt, J.H.Wang, G.Wang, H.Wu, Y.Greenlee, W.J.Parker, E.M.Kennedy, M.E.Stamford, A.W.

(2016) J Med Chem 59: 10435-10450

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b00307
  • Primary Citation of Related Structures:  
    5HTZ, 5HU0, 5HU1

  • PubMed Abstract: 

    Verubecestat 3 (MK-8931), a diaryl amide-substituted 3-imino-1,2,4-thiadiazinane 1,1-dioxide derivative, is a high-affinity β-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitor currently undergoing Phase 3 clinical evaluation for the treatment of mild to moderate and prodromal Alzheimer's disease. Although not selective over the closely related aspartyl protease BACE2, verubecestat has high selectivity for BACE1 over other key aspartyl proteases, notably cathepsin D, and profoundly lowers CSF and brain Aβ levels in rats and nonhuman primates and CSF Aβ levels in humans. In this annotation, we describe the discovery of 3, including design, validation, and selected SAR around the novel iminothiadiazinane dioxide core as well as aspects of its preclinical and Phase 1 clinical characterization.

  • Organizational Affiliation

    Albany Molecular Research Inc. , 26 Corporate Circle, Albany, New York 12203, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1
A, B
412Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
GTEx:  ENSG00000186318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.83 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.475α = 90
b = 89.822β = 90
c = 131.134γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2016-11-09 
  • Deposition Author(s): Orth, P.

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2016-11-30
    Changes: Database references
  • Version 1.2: 2017-01-04
    Changes: Database references