5HU0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


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

  • 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1AB412Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
NIH Common Fund Data Resources
PHAROS  P56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
66H
Query on 66H

Download Ideal Coordinates CCD File 
A, B
N-{3-[(2E,4R)-2-imino-1-methyl-5-oxo-4-phenylimidazolidin-4-yl]phenyl}furan-2-carboxamide
C21 H18 N4 O3
SOHROZVXKZYZIE-OAQYLSRUSA-N
 Ligand Interaction
TLA
Query on TLA

Download Ideal Coordinates CCD File 
A, B
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
66HKi:  595   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
BUSTERrefinement
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2016-01-27 
  • Released Date: 2016-11-09 
  • Deposition Author(s): Orth, P.

Revision History 

  • 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