7B1Q

Crystal Structure of Human BACE-1 in Complex with Compound NB-360 (compound 54)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Synthesis of the Potent, Selective, and Efficacious beta-Secretase (BACE1) Inhibitor NB-360.

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

(2021) J Med Chem 64: 4677-4696

  • DOI: 10.1021/acs.jmedchem.0c02143
  • Primary Citation of Related Structures:  
    7B1E, 7B1Q, 7B1P

  • PubMed Abstract: 
  • Starting from lead compound 4 , the 1,4-oxazine headgroup was optimized to improve potency and brain penetration. Focusing at the 6-position of the 5-amino-1,4-oxazine, the insertion of a Me and a CF 3 group delivered an excellent pharmacological profile with a p K a of 7 ...

    Starting from lead compound 4 , the 1,4-oxazine headgroup was optimized to improve potency and brain penetration. Focusing at the 6-position of the 5-amino-1,4-oxazine, the insertion of a Me and a CF 3 group delivered an excellent pharmacological profile with a p K a of 7.1 and a very low P-gp efflux ratio enabling high central nervous system (CNS) penetration and exposure. Various synthetic routes to access BACE1 inhibitors bearing a 5-amino-6-methyl-6-(trifluoromethyl)-1,4-oxazine headgroup were investigated. Subsequent optimization of the P3 fragment provided the highly potent N -(3-((3 R ,6 R )-5-amino-3,6-dimethyl-6-(trifluoromethyl)-3,6-dihydro-2 H -1,4-oxazin-3-yl)-4-fluorophenyl)-5-cyano-3-methylpicolinamide 54 ( NB-360 ), able to reduce significantly A β levels in mice, rats, and dogs in acute and chronic treatment regimens.


    Organizational Affiliation

    Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A402Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
NIH Common Fund Data Resources
PHAROS:  P56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SLK
Query on SLK

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[3-[(3~{R},6~{R})-5-azanyl-3,6-dimethyl-6-(trifluoromethyl)-2~{H}-1,4-oxazin-3-yl]-4-fluoranyl-phenyl]-5-cyano-3-methyl-pyridine-2-carboxamide
C21 H19 F4 N5 O2
BQFHTVUWPJXLOW-VQTJNVASSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.747α = 90
b = 74.158β = 90
c = 104.512γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CNXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release
  • Version 1.1: 2021-05-05
    Changes: Database references