8-Tetrahydropyran-2-yl chromans: highly selective beta-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitors

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


8-Tetrahydropyran-2-yl Chromans: Highly Selective Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1) Inhibitors.

Thomas, A.A.Hunt, K.W.Newhouse, B.Watts, R.J.Liu, X.Vigers, G.Smith, D.Rhodes, S.P.Brown, K.D.Otten, J.N.Burkard, M.Cox, A.A.Geck Do, M.K.Dutcher, D.Rana, S.DeLisle, R.K.Regal, K.Wright, A.D.Groneberg, R.Liao, J.Scearce-Levie, K.Siu, M.Purkey, H.E.Lyssikatos, J.P.

(2014) J Med Chem 57: 10112-10129

  • DOI: https://doi.org/10.1021/jm5015132
  • Primary Citation of Related Structures:  
    4R5N, 4RRN, 4RRO, 4RRS

  • PubMed Abstract: 

    A series of 2,3,4,4a,10,10a-hexahydropyrano[3,2-b]chromene analogs was developed that demonstrated high selectivity (>2000-fold) for BACE1 vs Cathepsin D (CatD). Three different Asp-binding moieties were examined: spirocyclic acyl guanidines, aminooxazolines, and aminothiazolines in order to modulate potency, selectivity, efflux, and permeability. Guided by structure based design, changes to P2' and P3 moieties were explored. A conformationally restricted P2' methyl group provided inhibitors with excellent cell potency (37-137 nM) and selectivity (435 to >2000-fold) for BACE1 vs CatD. These efforts lead to compound 59, which demonstrated a 69% reduction in rat CSF Aβ1-40 at 60 mg/kg (PO).

  • Organizational Affiliation

    Array BioPharma, 3200 Walnut Street, Boulder, Colorado 80301, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1406Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
PHAROS:  P56817
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 3UX

Download Ideal Coordinates CCD File 
C [auth A](4S,4a'R,10a'S)-2-amino-8'-(2-fluoropyridin-3-yl)-1,4a'-dimethyl-3',4',4a',10a'-tetrahydro-2'H-spiro[imidazole-4,10'-pyrano[3,2-b]chromen]-5(1H)-one
C21 H21 F N4 O3
Query on NI

Download Ideal Coordinates CCD File 
Binding Affinity Annotations 
IDSourceBinding Affinity
3UX BindingDB:  4RRO IC50: min: 26, max: 37 (nM) from 2 assay(s)
Binding MOAD:  4RRO IC50: 26 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.11α = 90
b = 104.08β = 90
c = 100.7γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2014-12-31
    Changes: Database references