3U6A

Rational Design and Synthesis of Aminopiperazinones as Beta Secretase (BACE) Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb3U6A/pdb

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


• Deposited: 2011-10-12 Released: 2011-11-09 
• Deposition Author(s): Spurlino, J.C., Alexander, R.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.237 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Literature

Rational design and synthesis of aminopiperazinones as beta-secretase (BACE) inhibitors.

Tresadern, G., Delgado, F., Delgado, O., Gijsen, H., Macdonald, G.J., Moechars, D., Rombouts, F., Alexander, R., Spurlino, J., Van Gool, M., Vega, J.A., Trabanco, A.A.

(2011) Bioorg Med Chem Lett 21: 7255-7260

• PubMed: 22071305 
• DOI: https://doi.org/10.1016/j.bmcl.2011.10.050
• Primary Citation of Related Structures:  
  3U6A


• PubMed Abstract: 
  

  Aminopiperazinone inhibitors of BACE were identified by rational design. Structure based design guided idea prioritization and initial racemic hit 18a showed good activity. Modification in decoration and chiral separation resulted in the 40 nM inhibitor, (-)-37, which showed in vivo reduction of amyloid beta peptides. The crystal structure of 18a showed a binding mode driven by interaction with the catalytic aspartate dyad and distribution of the biaryl amide decoration towards S1 and S3 pockets.

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Organizational Affiliation: 

Research Informatics & Integrative Genomics, Calle Jarama 75, Poligono Industrial, Toledo 45007, Spain. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 132.13 kDa 
• Atom Count: 9,761 
• Modelled Residue Count: 1,144 
• Deposited Residue Count: 1,170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B, C	390	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
18P	D [auth A], H [auth B], M [auth C]	N-{3-[(2R)-6-amino-2,4-dimethyl-3-oxo-2,3,4,5-tetrahydropyrazin-2-yl]phenyl}-5-chloropyridine-2-carboxamide C18 H18 Cl N5 O2 MRYFMHAPTQCQLE-GOSISDBHSA-N
SO4	E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B], N [auth C], O [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
18P	PDBBind:  3U6A	IC50: 324 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.237 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 225.3	α = 90
b = 104.45	β = 102.66
c = 66.76	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-09 
Deposition Author(s): Spurlino, J.C., Alexander, R.S.

Revision History  

• Version 1.0: 2011-11-09
  Type: Initial release
  
• Version 1.1: 2013-09-04
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary