7B1P

Crystal Structure of Human BACE-1 in Complex with Compound 38a (NB-854)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 

Starting Model: experimental
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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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SL8 (Subject of Investigation/LOI)
Query on SL8

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]phenyl]-5-bromanyl-pyridine-2-carboxamide
C19 H18 Br F3 N4 O2
YGNDEESWZOXXLA-ZWKOTPCHSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
SL8 BindingDB:  7B1P IC50: min: 20, max: 32 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.576α = 90
b = 74.805β = 90
c = 104.974γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CNSphasing

Structure Validation

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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: 2024-01-31
    Changes: Data collection, Database references, Refinement description