6EJ2

BACE1 compound 28


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Toward beta-Secretase-1 Inhibitors with Improved Isoform Selectivity.

Johansson, P.Kaspersson, K.Gurrell, I.K.Back, E.Eketjall, S.Scott, C.W.Cebers, G.Thorne, P.McKenzie, M.J.Beaton, H.Davey, P.Kolmodin, K.Holenz, J.Duggan, M.E.Budd Haeberlein, S.Burli, R.W.

(2018) J. Med. Chem. 61: 3491-3502

  • DOI: 10.1021/acs.jmedchem.7b01716
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • BACE1 is responsible for the first step in APP proteolysis, leading to toxic Aβ production, and has been indicated to play a key role in the pathogenesis of Alzheimer's disease. The related isoform BACE2 is thought to be involved in processing of the ...

    BACE1 is responsible for the first step in APP proteolysis, leading to toxic Aβ production, and has been indicated to play a key role in the pathogenesis of Alzheimer's disease. The related isoform BACE2 is thought to be involved in processing of the pigment cell-specific melanocyte protein. To avoid potential effects on pigmentation, we investigated the feasibility for developing isoform-selective BACE1 inhibitors. Cocrystal structures of 47 compounds were analyzed and clustered according to their selectivity profiles. Selective BACE1 inhibitors were found to exhibit two distinct conformational features proximal to the flap and the S3 subpocket. Several new molecules were designed and tested to make use of this observation. The combination of a pyrimidinyl C-ring and a methylcyclohexyl element resulted in lead molecule 28, which exhibited ∼50-fold selectivity. Compared to a nonselective BACE1/2 inhibitor, 28 showed significantly less inhibition of PMEL processing in human melanocytes, indicating good functional selectivity of this inhibitor class.


    Organizational Affiliation

    Sprint Bioscience , 141 57 Huddinge , Sweden.,Department of Food Science, National (Taiwan) Ocean University, Keelung, 202, Taiwan.,Biotechnology Center, National Chung Hsing University, Taichung City, 402, Taiwan.,Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan tendo@cc.kyoto-su.ac.jp.,Charnwood Molecular , Loughborough LE11 5DA , U.K.,Neuroscience, IMED Biotech Unit , AstraZeneca , Cambridge CB21 6GH , U.K.,Japan Science and Technology Agency/Core Research for Evolutional Science and Technology, Nagoya University, Nagoya, Japan.,Research Center for Materials Science, Nagoya University, Nagoya, Japan.,Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata, Japan.,Cardiovascular and Metabolic Diseases, IMED Biotech Unit , AstraZeneca , 141 57 Huddinge , Sweden.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, 112, Taiwan.,Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.,Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan.,Oncology Chemistry, IMED Biotech Unit , AstraZeneca , Cambridge CB4 0WG , U.K.,Institute of Biochemistry, ETH Zürich, Zürich, Switzerland.,Discovery Sciences, IMED Biotech Unit , AstraZeneca , S-43183 Mölndal , Sweden.,Japan Science and Technology Agency/Core Research for Evolutional Science and Technology, Kyoto Sangyo University, Kyoto, Japan.,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan.,Discovery Safety, Drug Safety and Metabolism, IMED Biotech Unit , AstraZeneca , Waltham , Massachusetts 02451 , United States.,Department of Biochemistry, National Centre of Competence in Research Chemical Biology, University of Geneva, Geneva, Switzerland.,Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A
501Homo 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
B7E
Query on B7E

Download SDF File 
Download CCD File 
A
compound 28
C22 H26 N4 O2
LNZBKHMXPFCMOB-GLYDZZHWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.206 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 101.580α = 90.00
b = 101.580β = 90.00
c = 170.730γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-09-20 
  • Released Date: 2018-04-18 
  • Deposition Author(s): Johansson, P.

Revision History 

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-05-09
    Type: Data collection, Database references