5HU1

BACE1 in complex with (R)-N-(3-(3-amino-2,5-dimethyl-1,1-dioxido-5,6-dihydro-2H-1,2,4-thiadiazin-5-yl)-4-fluorophenyl)-5-fluoropicolinamide

• PDB DOI:  https://doi.org/10.2210/pdb5HU1/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.201 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 

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

• PubMed: 27933948 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 92.78 kDa 
• Atom Count: 7,001 
• Modelled Residue Count: 774 
• Deposited Residue Count: 824 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B	412	Homo sapiens	Mutation(s): 0  Gene Names: BACE1, BACE, KIAA1149 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
66F	C [auth A], D [auth B]	N-{3-[(5R)-3-amino-2,5-dimethyl-1,1-dioxido-5,6-dihydro-2H-1,2,4-thiadiazin-5-yl]-4-fluorophenyl}-5-fluoropyridine-2-carboxamide C17 H17 F2 N5 O3 S YHYKUSGACIYRML-KRWDZBQOSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
66F	Binding MOAD:  5HU1	Ki: 2.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.201 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.05	α = 90
b = 90.2	β = 90
c = 131.36	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• 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