7N4N

BACE-2 in complex with ligand 36


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.163 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

JNJ-67569762, A 2-Aminotetrahydropyridine-Based Selective BACE1 Inhibitor Targeting the S3 Pocket: From Discovery to Clinical Candidate.

Rombouts, F.J.R.Kusakabe, K.I.Alexander, R.Austin, N.Borghys, H.De Cleyn, M.Dhuyvetter, D.Gijsen, H.J.M.Hrupka, B.Jacobs, T.Jerhaoui, S.Lammens, L.Leclercq, L.Tsubone, K.Ueno, T.Morimoto, K.Einaru, S.Sumiyoshi, H.Van den Bergh, A.Vos, A.Surkyn, M.Teisman, A.Moechars, D.

(2021) J Med Chem 64: 14175-14191

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00935
  • Primary Citation of Related Structures:  
    7N4N, 7N66

  • PubMed Abstract: 

    The discovery of a novel 2-aminotetrahydropyridine class of BACE1 inhibitors is described. Their pK a and lipophilicity were modulated by a pending sulfonyl group, while good permeability and brain penetration were achieved via intramolecular hydrogen bonding. BACE1 selectivity over BACE2 was achieved in the S3 pocket by a novel bicyclic ring system. An optimization addressing reactive metabolite formation, cardiovascular safety, and CNS toxicity is described, leading to the clinical candidate JNJ-67569762 ( 12 ), which gave robust dose-dependent BACE1-mediated amyloid β lowering without showing BACE2-dependent hair depigmentation in preclinical models. We show that 12 has a favorable projected human dose and PK and hence presented us with an opportunity to test a highly selective BACE1 inhibitor in humans. However, 12 was found to have a QT effect upon repeat dosing in dogs and its development was halted in favor of other selective leads, which will be reported in the future.


  • Organizational Affiliation

    Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, Beerse B-2340, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 2386Homo sapiensMutation(s): 0 
Gene Names: BACE2AEPLCALP56ASP21CDA13UNQ418/PRO852
EC: 3.4.23.45
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5Z0 (Homo sapiens)
Explore Q9Y5Z0 
Go to UniProtKB:  Q9Y5Z0
PHAROS:  Q9Y5Z0
GTEx:  ENSG00000182240 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y5Z0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
XaperoneB [auth D]114Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
0BK BindingDB:  7N4N IC50: 189 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.757α = 90
b = 74.492β = 90
c = 109.361γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2021-10-27
    Changes: Database references