5CLM

1,4-Oxazine BACE1 inhibitors

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

1,4-Oxazine beta-Secretase 1 (BACE1) Inhibitors: From Hit Generation to Orally Bioavailable Brain Penetrant Leads.

Rombouts, F.J., Tresadern, G., Delgado, O., Martinez-Lamenca, C., Van Gool, M., Garcia-Molina, A., Alonso de Diego, S.A., Oehlrich, D., Prokopcova, H., Alonso, J.M., Austin, N., Borghys, H., Van Brandt, S., Surkyn, M., De Cleyn, M., Vos, A., Alexander, R., Macdonald, G., Moechars, D., Gijsen, H., Trabanco, A.A.

(2015) J Med Chem 58: 8216-8235

  • DOI: 10.1021/acs.jmedchem.5b01101
  • Primary Citation of Related Structures:  
    5CLM

  • PubMed Abstract: 

    • 1,4-Oxazines are presented, which show good in vitro inhibition in enzymatic and cellular BACE1 assays. We describe lead optimization focused on reducing the amidine pKa while optimizing interactions in the BACE1 active site. Our strategy permitted m ...

    1,4-Oxazines are presented, which show good in vitro inhibition in enzymatic and cellular BACE1 assays. We describe lead optimization focused on reducing the amidine pKa while optimizing interactions in the BACE1 active site. Our strategy permitted modulation of properties such as permeation and especially P-glycoprotein efflux. This led to compounds which were orally bioavailable, centrally active, and which demonstrated robust lowering of brain and CSF Aβ levels, respectively, in mouse and dog models. The amyloid lowering potential of these molecules makes them valuable leads in the search for new BACE1 inhibitors for the treatment of Alzheimer's disease.

    Organizational Affiliation: 

    Neuroscience Medicinal Chemistry, Janssen Research & Development, Janssen-Cilag SA , C/Jarama 75A, 45007 Toledo, Spain.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A401Homo sapiensMutation(s): 2 
Gene Names: BACE1, BACE, KIAA1149
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
NIH Common Fund Data Resources
PHAROS  P56817
GTEx  ENSG00000186318
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
52K
Query on 52K
Download Ideal Coordinates CCD File 
A
N-{3-[(3R)-5-amino-3-methyl-3,6-dihydro-2H-1,4-oxazin-3-yl]phenyl}-5-chloropyridine-2-carboxamide
C17 H17 Cl N4 O2
ZZUPAAPYPBQGKS-KRWDZBQOSA-N		 Ligand Interaction
IOD
Query on IOD
Download Ideal Coordinates CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
52KIC50:  44   nM  BindingDB
52KIC50:  240   nM  BindingDB
52KIC50:  9.100000381469727   nM  BindingDB
52KIC50:  7.400000095367432   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.824α = 90
b = 100.824β = 90
c = 170.104γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2015-11-04
    Changes: Database references