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


Ligand Structure Quality Assessment 


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 modulation of properties such as permeation and especially P-glycoprotein efflux ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A401Homo sapiensMutation(s): 2 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
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 
B [auth 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 
C [auth A],
D [auth A],
E [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
52K BindingDB:  5CLM IC50: min: 7.4, max: 240 (nM) from 4 assay(s)
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



Ligand Structure Quality Assessment 



Entry History 

Revision History  (Full details and data files)

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