4DUS

Structure of Bace-1 (Beta-Secretase) in complex with N-((2S,3R)-1-(4-fluorophenyl)-3-hydroxy-4-((6'-neopentyl-3',4'-dihydrospiro[cyclobutane-1,2'-pyrano[2,3-b]pyridin]-4'-yl)amino)butan-2-yl)acetamide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

A Potent and Orally Efficacious, Hydroxyethylamine-Based Inhibitor of beta-Secretase.

Kaller, M.R., Harried, S.S., Albrecht, B., Amarante, P., Babu-Khan, S., Bartberger, M.D., Brown, J., Brown, R., Chen, K., Cheng, Y., Citron, M., Croghan, M.D., Graceffa, R., Hickman, D., Judd, T., Kriemen, C., La, D., Li, V., Lopez, P., Luo, Y., Masse, C., Monenschein, H., Nguyen, T., Pennington, L.D., Miguel, T.S., Sickmier, E.A., Wahl, R.C., Weiss, M.M., Wen, P.H., Williamson, T., Wood, S., Xue, M., Yang, B., Zhang, J., Patel, V., Zhong, W., Hitchcock, S.

(2012) ACS Med Chem Lett 3: 886-891

  • DOI: 10.1021/ml3000148
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • β-Secretase inhibitors are potentially disease-modifying treatments for Alzheimer's disease. Previous efforts in our laboratory have resulted in hydroxyethylamine-derived inhibitors such as 1 with low nanomolar potency against β-site amyloid precurso ...

    β-Secretase inhibitors are potentially disease-modifying treatments for Alzheimer's disease. Previous efforts in our laboratory have resulted in hydroxyethylamine-derived inhibitors such as 1 with low nanomolar potency against β-site amyloid precursor protein cleaving enzyme (BACE). When dosed intravenously, compound 1 was also shown to significantly reduce Aβ40 levels in plasma, brain, and cerebral spinal fluid. Herein, we report further optimizations that led to the discovery of inhibitor 16 as a novel, potent, and orally efficacious BACE inhibitor.

    Organizational Affiliation: 

    Chemistry Research and Discovery, Department of Molecular Structure, Department of Neuroscience, Department of HTS and Molecular Pharmacology, and Department of Pharmacokinetics and Drug Metabolism, Amgen Inc. , One Amgen Center Drive, Thousand Oaks, California 91320, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A
411Homo sapiensMutation(s): 0 
Gene Names: BACE1 (BACE, KIAA1149)
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Go to Gene View: BACE1
Go to UniProtKB:  P56817
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD
Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
0MP
Query on 0MP
Download SDF File 
Download CCD File 
A
N-((2S,3R)-1-(4-fluorophenyl)-3-hydroxy-4-((6'-neopentyl-3',4'-dihydrospiro[cyclobutane-1,2'-pyrano[2,3-b]pyridin]-4'-yl)amino)butan-2-yl)acetamide
C28 H38 F N3 O3
FBJQDUYQPYABBR-CCDWMCETSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0MPIC50: 5 - 13 nM (99) BINDINGDB
OMPIC50: 5 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.221 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.309α = 90.00
b = 102.309β = 90.00
c = 169.758γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
BOSdata collection
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2012-02-22 
  • Released Date: 2012-10-10 
  • Deposition Author(s): Sickmier, E.A.

Revision History 

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2014-07-02
    Type: Database references