CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH 5-Cyano-pyridine-2-carboxylic acid [3-((S)-2-amino-4-methyl-5,6-dihydro-4H-[1,3]oxazin-4-yl)-4-fluoro-phenyl]-amide

Experimental Data Snapshot

  • Resolution: 1.97 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


beta-Secretase (BACE1) inhibitors with high in vivo efficacy suitable for clinical evaluation in Alzheimer's disease.

Hilpert, H.Guba, W.Woltering, T.J.Wostl, W.Pinard, E.Mauser, H.Mayweg, A.V.Rogers-Evans, M.Humm, R.Krummenacher, D.Muser, T.Schnider, C.Jacobsen, H.Ozmen, L.Bergadano, A.Banner, D.W.Hochstrasser, R.Kuglstatter, A.David-Pierson, P.Fischer, H.Polara, A.Narquizian, R.

(2013) J Med Chem 56: 3980-3995

  • DOI: https://doi.org/10.1021/jm400225m
  • Primary Citation of Related Structures:  
    3ZLQ, 3ZMG, 4J0P, 4J0T, 4J0V, 4J0Y, 4J0Z, 4J17, 4J1C, 4J1E, 4J1F, 4J1H, 4J1I, 4J1K

  • PubMed Abstract: 

    An extensive fluorine scan of 1,3-oxazines revealed the power of fluorine(s) to lower the pKa and thereby dramatically change the pharmacological profile of this class of BACE1 inhibitors. The CF3 substituted oxazine 89, a potent and highly brain penetrant BACE1 inhibitor, was able to reduce significantly CSF Aβ40 and 42 in rats at oral doses as low as 1 mg/kg. The effect was long lasting, showing a significant reduction of Aβ40 and 42 even after 24 h. In contrast to 89, compound 1b lacking the CF3 group was virtually inactive in vivo.

  • Organizational Affiliation

    Discovery Chemistry, Pharma Research & Early Development, Grenzacherstrasse 124, Basel CH-4070, Switzerland. hans.hilpert@roche.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1409Homo sapiensMutation(s): 1 
Gene Names: BACE1BACEKIAA1149
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
PHAROS:  P56817
GTEx:  ENSG00000186318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
1H8 BindingDB:  4J0P IC50: min: 3.7, max: 118 (nM) from 5 assay(s)
PDBBind:  4J0P IC50: 51 (nM) from 1 assay(s)
Binding MOAD:  4J0P IC50: 51 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.97 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.537α = 90
b = 102.537β = 90
c = 169.795γ = 120
Software Package:
Software NamePurpose
RemDAqdata collection
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description