4XKX

Crystal structure of BACE1 in complex with 2-aminooxazoline 3-azaxanthene inhibitor 28


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Development of 2-aminooxazoline 3-azaxanthenes as orally efficacious beta-secretase inhibitors for the potential treatment of Alzheimer's disease.

Chen, J.J.Liu, Q.Yuan, C.Gore, V.Lopez, P.Ma, V.Amegadzie, A.Qian, W.Judd, T.C.Minatti, A.E.Brown, J.Cheng, Y.Xue, M.Zhong, W.Dineen, T.A.Epstein, O.Human, J.Kreiman, C.Marx, I.Weiss, M.M.Hitchcock, S.A.Powers, T.S.Chen, K.Wen, P.H.Whittington, D.A.Cheng, A.C.Bartberger, M.D.Hickman, D.Werner, J.A.Vargas, H.M.Everds, N.E.Vonderfecht, S.L.Dunn, R.T.Wood, S.Fremeau, R.T.White, R.D.Patel, V.F.

(2015) Bioorg Med Chem Lett 25: 767-774

  • DOI: 10.1016/j.bmcl.2014.12.092
  • Primary Citation of Related Structures:  
    4XKX

  • PubMed Abstract: 
  • The β-site amyloid precursor protein (APP) cleaving enzyme 1 (BACE1) is one of the most hotly pursued targets for the treatment of Alzheimer's disease. We used a structure- and property-based drug design approach to identify 2-aminooxazoline 3-azaxan ...

    The β-site amyloid precursor protein (APP) cleaving enzyme 1 (BACE1) is one of the most hotly pursued targets for the treatment of Alzheimer's disease. We used a structure- and property-based drug design approach to identify 2-aminooxazoline 3-azaxanthenes as potent BACE1 inhibitors which significantly reduced CSF and brain Aβ levels in a rat pharmacodynamic model. Compared to the initial lead 2, compound 28 exhibited reduced potential for QTc prolongation in a non-human primate cardiovascular safety model.


    Organizational Affiliation

    Department of Medicinal Chemistry, Amgen Inc., 360 Binney Street, Cambridge, MA 02142, USA.



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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
43K
Query on 43K

Download CCD File 
A
(5S)-7-(2-fluoropyridin-3-yl)-3-(2-fluoropyridin-4-yl)spiro[chromeno[2,3-c]pyridine-5,4'-[1,3]oxazol]-2'-amine
C24 H15 F2 N5 O2
LEFDLEYZSDTVMO-DEOSSOPVSA-N
 Ligand Interaction
IOD
Query on IOD

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

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
43KIC50:  21   nM  BindingDB
43KIC50:  0.8999999761581421   nM  Binding MOAD
43KIC50:  0.8999999761581421   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.148α = 90
b = 102.148β = 90
c = 170.894γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-02-18
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description, Source and taxonomy