3U6A

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

    Research Informatics & Integrative Genomics, Calle Jarama 75, Poligono Industrial, Toledo 45007, Spain. gtresade@its.jnj.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1ABC390Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
NIH Common Fund Data Resources
PHAROS  P56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
18P
Query on 18P

Download CCD File 
A, B, 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
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
18PIC50:  447   nM  BindingDB
18PIC50:  98   nM  BindingDB
18PIC50:  36   nM  BindingDB
18PIC50:  37   nM  BindingDB
18PIC50 :  324   nM  PDBBind
18PIC50:  78   nM  BindingDB
18PIC50:  324   nM  BindingDB
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 = 225.3α = 90
b = 104.45β = 102.66
c = 66.76γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-09
    Type: Initial release
  • Version 1.1: 2013-09-04
    Changes: Database references