4WY1

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1021/jm501833t
  • Primary Citation of Related Structures:  

  • 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, dist ...

    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

    #Departamento de Inovação, Eurofarma Laboratorios S.A., Avenida Vereador José Diniz, 3465, Campo Belo, São Paulo, Brasil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A
404Homo sapiensMutation(s): 0 
Gene Names: BACE1 (BACE, KIAA1149)
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Go to Gene View: BACE1
Go to UniProtKB:  P56817
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3VO
Query on 3VO

Download SDF File 
Download CCD File 
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3VOIC50: 265 - 6700 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.167 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 74.856α = 90.00
b = 103.719β = 90.00
c = 100.579γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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