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: 2.50 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

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Ligand Structure Quality Assessment 


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:  
    4DUS, 4FS4

  • 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 precursor protein cleaving enzyme (BACE) ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A411Homo sapiensMutation(s): 0 
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
GTEx:  ENSG00000186318
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0MP (Subject of Investigation/LOI)
Query on 0MP
Download Ideal Coordinates CCD File 
K [auth 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
IOD
Query on IOD
Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
I [auth A], J [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
0MP BindingDB:  4DUS IC50: min: 5, max: 13 (nM) from 4 assay(s)
OMP PDBBind:  4DUS IC50: 5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.309α = 90
b = 102.309β = 90
c = 169.758γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
BOSdata collection
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  


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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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