6FGY

Crystal Structure of Human BACE-1 in Complex with amino-1,4-oxazine compound 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.204 

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Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

Discovery of amino-1,4-oxazines as potent BACE-1 inhibitors.

Veenstra, S.J.Rueeger, H.Voegtle, M.Lueoend, R.Holzer, P.Hurth, K.Tintelnot-Blomley, M.Frederiksen, M.Rondeau, J.M.Jacobson, L.Staufenbiel, M.Neumann, U.Machauer, R.

(2018) Bioorg Med Chem Lett 28: 2195-2200

  • DOI: https://doi.org/10.1016/j.bmcl.2018.05.003
  • Primary Citation of Related Structures:  
    6FGY

  • PubMed Abstract: 

    New amino-1,4-oxazine derived BACE-1 inhibitors were explored and various synthetic routes developed. The binding mode of the inhibitors was elucidated by co-crystallization of 4 with BACE-1 and X-ray analysis. Subsequent optimization led to inhibitors with low double digit nanomolar activity in a biochemical and single digit nanomolar potency in a cellular assays. To assess the inhibitors for their permeation properties and potential to cross the blood-brain-barrier a MDR1-MDCK cell model was successfully applied. Compound 8a confirmed the in vitro results by dose-dependently reducing Aβ levels in mice in an acute treatment regimen.


  • Organizational Affiliation

    Department of Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1396Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
EC: 3.4.23.46
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D9W (Subject of Investigation/LOI)
Query on D9W

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[3-[(3~{R})-5-azanyl-3-methyl-2,6-dihydro-1,4-oxazin-3-yl]phenyl]-5-bromanyl-pyridine-2-carboxamide
C17 H17 Br N4 O2
HALWMQVNBCAXRZ-KRWDZBQOSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.056α = 90
b = 76.738β = 90
c = 104.214γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
CNXrefinement
PDB_EXTRACTdata extraction
CNXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted D9WClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Structure summary