4RCD

Crystal structure of BACE1 in complex with a 2-aminooxazoline 4-azaxanthene inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

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Literature

Inhibitors of beta-Site Amyloid Precursor Protein Cleaving Enzyme (BACE1): Identification of (S)-7-(2-Fluoropyridin-3-yl)-3-((3-methyloxetan-3-yl)ethynyl)-5'H-spiro[chromeno[2,3-b]pyridine-5,4'-oxazol]-2'-amine (AMG-8718).

Dineen, T.A., Chen, K., Cheng, A.C., Derakhchan, K., Epstein, O., Esmay, J., Hickman, D., Kreiman, C.E., Marx, I.E., Wahl, R.C., Wen, P.H., Weiss, M.M., Whittington, D.A., Wood, S., Fremeau, R.T., White, R.D., Patel, V.F.

(2014) J Med Chem 57: 9811-9831

  • DOI: 10.1021/jm5012676
  • Primary Citation of Related Structures:  
    4RCD

  • PubMed Abstract: 

    • We have previously shown that the aminooxazoline xanthene scaffold can generate potent and orally efficacious BACE1 inhibitors although certain of these compounds exhibited potential hERG liabilities. In this article, we describe 4-aza substitution on the xanthene core as a means to increase BACE1 potency while reducing hERG binding affinity ...

    We have previously shown that the aminooxazoline xanthene scaffold can generate potent and orally efficacious BACE1 inhibitors although certain of these compounds exhibited potential hERG liabilities. In this article, we describe 4-aza substitution on the xanthene core as a means to increase BACE1 potency while reducing hERG binding affinity. Further optimization of the P3 and P2' side chains resulted in the identification of 42 (AMG-8718), a compound with a balanced profile of BACE1 potency, hERG binding affinity, and Pgp recognition. This compound produced robust and sustained reductions of CSF and brain Aβ levels in a rat pharmacodynamic model and exhibited significantly reduced potential for QTc elongation in a cardiovascular safety model.

    Organizational Affiliation: 

    Departments of Therapeutic Discovery, ‡Neuroscience, §Molecular Structure and Characterization, ∥Pharmacokinetics and Drug Metabolism, and ⊥Comparative Biology and Safety Sciences, Amgen, Inc. , 360 Binney Street, Cambridge, Massachusetts 02142, and One Amgen Center Drive, Thousand Oaks, California 91320, United States.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A411Homo sapiensMutation(s): 2 
Gene Names: BACE, BACE1, 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3LL
Query on 3LL
Download Ideal Coordinates CCD File 
B [auth A](5S)-7-(2-fluoropyridin-3-yl)-3-[(3-methyloxetan-3-yl)ethynyl]spiro[chromeno[2,3-b]pyridine-5,4'-[1,3]oxazol]-2'-amine
C25 H19 F N4 O3
GKKFBOARESVMBW-VWLOTQADSA-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
GOL
Query on GOL
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3LL Binding MOAD:  4RCD IC50: 0.7 (nM) from 1 assay(s)
BindingDB:  4RCD IC50: min: 0.7, max: 4.4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.607α = 90
b = 102.607β = 90
c = 170.671γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
DENZOdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-21
    Type: Initial release