Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.39 kDa 
• Atom Count: 3062 
• Modelled Residue Count: 376 
• Deposited Residue Count: 401 
• Unique protein chains: 1

5CLM

1,4-Oxazine BACE1 inhibitors

• PDB DOI: 10.2210/pdb5CLM/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-07-16 Released: 2015-09-30 
• Deposition Author(s): Rombouts, F., Tresadern, G., Delgado, O., Martinez Lamenca, C., Van Gool, M., Garcia-Molina, A., Alonso De Diego, S., 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., Trabanco, A., Gijsen, H.

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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 

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

• PubMed: 26378740 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	401	Homo sapiens	Mutation(s): 2  Gene Names: BACE1, BACE, KIAA1149 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
52K	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
IOD	C [auth A], D [auth A], E [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding 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 = 100.824	α = 90
b = 100.824	β = 90
c = 170.104	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-07-16 
• Released Date: 2015-09-30 
Deposition Author(s): Rombouts, F., Tresadern, G., Delgado, O., Martinez Lamenca, C., Van Gool, M., Garcia-Molina, A., Alonso De Diego, S., 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., Trabanco, A., Gijsen, H.

Revision History  

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