4WY1

Crystal structure of human BACE-1 bound to Compound 24B

• PDB DOI:  https://doi.org/10.2210/pdb4WY1/pdb

• Classification: Hydrolase/hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-11-14 Released: 2015-03-04 
• Deposition Author(s): Vajdos, F.F., Parris, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.220 
• R-Value Work: 0.167 
• R-Value Observed: 0.170 

Literature

Discovery of a Series of Efficient, Centrally Efficacious BACE1 Inhibitors through Structure-Based Drug Design.

Butler, C.R., Brodney, M.A., Beck, E.M., Barreiro, G., Nolan, C.E., Pan, F., Vajdos, F., Parris, K., Varghese, A.H., Helal, C.J., Lira, R., Doran, S.D., Riddell, D.R., Buzon, L.M., Dutra, J.K., Martinez-Alsina, L.A., Ogilvie, K., Murray, J.C., Young, J.M., Atchison, K., Robshaw, A., Gonzales, C., Wang, J., Zhang, Y., O'Neill, B.T.

(2015) J Med Chem 58: 2678-2702

• PubMed: 25695670 
• DOI: https://doi.org/10.1021/jm501833t
• Primary Citation of Related Structures:  
  4WY1, 4WY6, 4X2L


• PubMed Abstract: 
  

The identification of centrally efficacious β-secretase (BACE1) inhibitors for the treatment of Alzheimer's disease (AD) has historically been thwarted by an inability to maintain alignment of potency, brain availability, and desired absorption, distribution, metabolism, and excretion (ADME) properties. In this paper, we describe a series of truncated, fused thioamidines that are efficiently selective in garnering BACE1 activity without simultaneously inhibiting the closely related cathepsin D or negatively impacting brain penetration and ADME alignment, as exemplified by 36. Upon oral administration, these inhibitors exhibit robust brain availability and are efficacious in lowering central Amyloid β (Aβ) levels in mouse and dog. In addition, chronic treatment in aged PS1/APP mice effects a decrease in the number and size of Aβ-derived plaques. Most importantly, evaluation of 36 in a 2-week exploratory toxicology study revealed no accumulation of autofluorescent material in retinal pigment epithelium or histology findings in the eye, issues observed with earlier BACE1 inhibitors.

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Organizational Affiliation: 

∇WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 45.44 kDa 
• Atom Count: 3,505 
• Modelled Residue Count: 394 
• Deposited Residue Count: 404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	404	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
3VO	B [auth A]	(4aR,8aS)-8a-(2,4-difluorophenyl)-4,4a,5,6,8,8a-hexahydropyrano[3,4-d][1,3]thiazin-2-amine C13 H14 F2 N2 O S CUNQNADGWRXYCV-SDBXPKJASA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3VO	BindingDB:  4WY1	IC50: min: 265, max: 6700 (nM) from 3 assay(s)
	Binding MOAD:  4WY1	IC50: 5100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.220 
• R-Value Work: 0.167 
• R-Value Observed: 0.170 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.856	α = 90
b = 103.719	β = 90
c = 100.579	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-04 
Deposition Author(s): Vajdos, F.F., Parris, K.

Revision History  

• Version 1.0: 2015-03-04
  Type: Initial release
  
• Version 1.1: 2015-04-08
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary