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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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: 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 ...

    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. Electronic address: rainer.machauer@novartis.com.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A396Homo sapiensMutation(s): 0 
Gene Names: BACE1, BACE, KIAA1149
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / 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		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
D9W Binding MOAD:  6FGY IC50: 70 (nM) from 1 assay(s)
BindingDB:  6FGY IC50: min: 17, max: 140 (nM) from 3 assay(s)
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

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Ligand Structure Quality Assessment 


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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