BACE1 compound 28

Experimental Data Snapshot

  • Resolution: 1.46 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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This is version 1.1 of the entry. See complete history


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: https://doi.org/10.1021/acs.jmedchem.7b01716
  • Primary Citation of Related Structures:  
    6EJ2, 6EJ3

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1501Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on B7E

Download Ideal Coordinates CCD File 
B [auth A]compound 28
C22 H26 N4 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
B7E Binding MOAD:  6EJ2 Ki: 16 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.46 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.58α = 90
b = 101.58β = 90
c = 170.73γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

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