4DUS | pdb_00004dus

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

• PDB DOI: https://doi.org/10.2210/pdb4DUS/pdb

• Classification: HYDROLASE/Hydrolase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.289 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

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

• PubMed: 24900403 
• DOI: https://doi.org/10.1021/ml3000148
• Primary Citation 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). 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.

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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.
Chemistry Research and Discovery, Amgen Inc. , One Kendall Square Building 1000, Cambridge, Massachusetts 02139, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 47.38 kDa 
• Atom Count: 2,982 
• Modeled Residue Count: 365 
• Deposited Residue Count: 411 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	411	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0MP	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
IOD	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
GOL	I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0MP	BindingDB:  4DUS	IC50: min: 5, max: 13 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.289 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.309	α = 90
b = 102.309	β = 90
c = 169.758	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BOS	data collection
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary