5HTZ

BACE1 in complex with (S)-5-(3-chloro-5-(5-(prop-1-yn-1-yl)pyridin-3-yl)thiophen-2-yl)-2,5-dimethyl-1,2,4-thiadiazinan-3-iminium 1,1-dioxide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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.


Macromolecules
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
EC: 3.4.23.46
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
PHAROS:  P56817
GTEx:  ENSG00000186318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
66J
Query on 66J

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(3E,5S)-5-{3-chloro-5-[5-(prop-1-yn-1-yl)pyridin-3-yl]thiophen-2-yl}-2,5-dimethyl-1,2,4-thiadiazinan-3-imine 1,1-dioxide
C17 H17 Cl N4 O2 S2
VKVMIZCLMUKTTA-KRWDZBQOSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.353α = 90
b = 89.978β = 90
c = 131.636γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
AMoREphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



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