6OD6

Structure of BACE-1 in complex with Ligand 13

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

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Literature

Evaluation of a Series of beta-Secretase 1 Inhibitors Containing Novel Heteroaryl-Fused-Piperazine Amidine Warheads.

Oehlrich, D., Peschiulli, A., Tresadern, G., Van Gool, M., Vega, J.A., De Lucas, A.I., Alonso de Diego, S.A., Prokopcova, H., Austin, N., Van Brandt, S., Surkyn, M., De Cleyn, M., Vos, A., Rombouts, F.J.R., Macdonald, G., Moechars, D., Gijsen, H.J.M., Trabanco, A.A.

(2019) ACS Med Chem Lett 10: 1159-1165

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00181
  • Primary Citation of Related Structures:  
    6OD6

  • PubMed Abstract: 

    • Despite several years of research, only a handful of β-secretase (BACE) 1 inhibitors have entered clinical trials as potential therapeutics against Alzheimer's disease. The intrinsic basic nature of low molecular weight, amidine-containing BACE 1 inhibitors makes them far from optimal as central nervous system drugs ...

    Despite several years of research, only a handful of β-secretase (BACE) 1 inhibitors have entered clinical trials as potential therapeutics against Alzheimer's disease. The intrinsic basic nature of low molecular weight, amidine-containing BACE 1 inhibitors makes them far from optimal as central nervous system drugs. Herein we present a set of novel heteroaryl-fused piperazine amidine inhibitors designed to lower the basicity of the key, enzyme binding, amidine functionality. This study resulted in the identification of highly potent (IC 50 ≤ 10 nM), permeable lead compounds with a reduced propensity to suffer from P-glycoprotein-mediated efflux.

    Organizational Affiliation: 

    Discovery Sciences Medicinal Chemistry, Janssen Research & Development, Janssen-Cilag S.A., C/Jarama 75A, 45007 Toledo, Spain.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1
A, B, C
432Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M7D
Query on M7D
Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
G [auth C]		N-{3-[(3R)-1-amino-3-methyl-3,4-dihydropyrrolo[1,2-a]pyrazin-3-yl]-4-fluorophenyl}-5-cyanopyridine-2-carboxamide
C21 H17 F N6 O
FZFJUKOAGOAQFB-NRFANRHFSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
F [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
M7D Binding MOAD:  6OD6 IC50: 10 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 232.398α = 90
b = 100.391β = 103.67
c = 64.606γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-25
    Type: Initial release