7B1E | pdb_00007b1e

BACE1 IN COMPLEX WITH compound 3 (NB-641)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 
    0.211 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.180 (DCC) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/acs.jmedchem.0c02143
  • Primary Citation of Related Structures:  
    7B1E, 7B1P, 7B1Q

  • 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 7.1 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1402Homo 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
SKW (Subject of Investigation/LOI)
Query on SKW

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[3-[(4~{S})-2-azanyl-4-methyl-5,6-dihydro-1,3-thiazin-4-yl]phenyl]-5-bromanyl-pyridine-2-carboxamide
C17 H17 Br N4 O S
FSIYTVBWWROBPT-KRWDZBQOSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
SKW BindingDB:  7B1E IC50: 37 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.180 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.686α = 90
b = 73.575β = 90
c = 103.983γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Structure summary