5UYU

Crystal structure of BACE1 in complex with 2-aminooxazoline-3-azaxanthene compound 12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Development of 2-aminooxazoline 3-azaxanthene beta-amyloid cleaving enzyme (BACE) inhibitors with improved selectivity against Cathepsin D.

Low, J.D.Bartberger, M.D.Chen, K.Cheng, Y.Fielden, M.R.Gore, V.Hickman, D.Liu, Q.Allen Sickmier, E.Vargas, H.M.Werner, J.White, R.D.Whittington, D.A.Wood, S.Minatti, A.E.

(2017) Medchemcomm 8: 1196-1206

  • DOI: 10.1039/c7md00106a
  • Primary Citation of Related Structures:  
    5UX4, 5UYU

  • PubMed Abstract: 
  • As part of an ongoing effort at Amgen to develop a disease-modifying therapy for Alzheimer's disease, we have previously used the aminooxazoline xanthene (AOX) scaffold to generate potent and orally efficacious BACE1 inhibitors. While AOX-BACE1 inhib ...

    As part of an ongoing effort at Amgen to develop a disease-modifying therapy for Alzheimer's disease, we have previously used the aminooxazoline xanthene (AOX) scaffold to generate potent and orally efficacious BACE1 inhibitors. While AOX-BACE1 inhibitors demonstrated acceptable cardiovascular safety margins, a retinal pathological finding in rat toxicological studies demanded further investigation. It has been widely postulated that such retinal toxicity might be related to off-target inhibition of Cathepsin D (CatD), a closely related aspartyl protease. We report the development of AOX-BACE1 inhibitors with improved selectivity against CatD by following a structure- and property-based approach. Our efforts culminated in the discovery of a picolinamide-substituted 3-aza-AOX-BACE1 inhibitor absent of retinal effects in an early screening rat toxicology study.


    Organizational Affiliation

    Department of Medicinal Chemistry , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA . Email: aminatti@amgen.com ; Tel: +1 805 447 4721.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A411Homo sapiensMutation(s): 2 
Gene Names: BACE1BACEKIAA1149
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
NIH Common Fund Data Resources
PHAROS  P56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8QV
Query on 8QV

Download Ideal Coordinates CCD File 
A
(5S)-3-(3,6-dihydro-2H-pyran-4-yl)-7-[5-(prop-1-yn-1-yl)pyridin-3-yl]-5'H-spiro[1-benzopyrano[2,3-c]pyridine-5,4'-[1,3]oxazol]-2'-amine
C27 H22 N4 O3
PAMPHNBKOPBUKU-MHZLTWQESA-N
 Ligand Interaction
IOD
Query on IOD

Download Ideal Coordinates CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.287α = 90
b = 102.287β = 90
c = 170.374γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2018-08-29
    Changes: Data collection, Database references, Derived calculations