Crystal structure of human BACE-1 bound to Compound 36

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

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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

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1415Homo 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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 3VP

Download Ideal Coordinates CCD File 
B [auth A](4aR,6R,8aS)-8a-(2,4-difluorophenyl)-6-(fluoromethyl)-4,4a,5,6,8,8a-hexahydropyrano[3,4-d][1,3]thiazin-2-amine
C14 H15 F3 N2 O S
Query on IOD

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
Query on DMS

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
K [auth A]
C2 H6 O S
Binding Affinity Annotations 
IDSourceBinding Affinity
3VP BindingDB:  4WY6 IC50: min: 61, max: 1390 (nM) from 3 assay(s)
Binding MOAD:  4WY6 IC50: 1070 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.871α = 90
b = 102.871β = 90
c = 170.884γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • 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