6UVP

BACE-1 in complex with compound #3

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.138 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Preparation and biological evaluation of BACE1 inhibitors: Leveraging trans-cyclopropyl moieties as ligand efficient conformational constraints.

Winneroski, L.L., Erickson, J.A., Green, S.J., Lopez, J.E., Stout, S.L., Porter, W.J., Timm, D.E., Audia, J.E., Barberis, M., Beck, J.P., Boggs, L.N., Borders, A.R., Boyer, R.D., Brier, R.A., Hembre, E.J., Hendle, J., Garcia-Losada, P., Minguez, J.M., Mathes, B.M., May, P.C., Monk, S.A., Rankovic, Z., Shi, Y., Watson, B.M., Yang, Z., Mergott, D.J.

(2020) Bioorg Med Chem 28: 115194-115194

  • DOI: https://doi.org/10.1016/j.bmc.2019.115194
  • Primary Citation of Related Structures:  
    6UVP, 6UVV, 6UVY, 6UWP, 6UWV

  • PubMed Abstract: 

    • Inhibition of BACE1 has become an important strategy in the quest for disease modifying agents to slow the progression of Alzheimer's disease. We previously reported the fragment-based discovery of LY2811376, the first BACE1 inhibitor reported to demonstrate robust reduction of human CSF Aβ in a Phase I clinical trial ...

    Inhibition of BACE1 has become an important strategy in the quest for disease modifying agents to slow the progression of Alzheimer's disease. We previously reported the fragment-based discovery of LY2811376, the first BACE1 inhibitor reported to demonstrate robust reduction of human CSF Aβ in a Phase I clinical trial. We also reported on the discovery of LY2886721, a potent BACE1 inhibitor that reached phase 2 clinical trials. Herein we describe the preparation and structure activity relationships (SAR) of a series of BACE1 inhibitors utilizing trans-cyclopropyl moieties as conformational constraints. The design, details of the stereochemically complex organic synthesis, and biological activity of these BACE1 inhibitors is described.

    Organizational Affiliation: 

    Lilly Research Laboratories, A Division of Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA. Electronic address: mergottdu@lilly.com.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1
A, B
442Homo 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QJM (Subject of Investigation/LOI)
Query on QJM
Download Ideal Coordinates CCD File 
D [auth A],
K [auth B]		N-{(1R,2R)-2-[(4aS,7aR)-2-amino-4a,5-dihydro-4H-furo[3,4-d][1,3]thiazin-7a(7H)-yl]cyclopropyl}-5-fluoropyridine-2-carboxamide
C15 H17 F N4 O2 S
OWWIYTVWTQBRDL-RAAPYIGPSA-N		 Ligand Interaction
QJJ (Subject of Investigation/LOI)
Query on QJJ
Download Ideal Coordinates CCD File 
C [auth A],
H [auth B],
I [auth B],
J [auth B]		N-{(1S,2S)-2-[(4aS,7aR)-2-amino-4a,5-dihydro-4H-furo[3,4-d][1,3]thiazin-7a(7H)-yl]cyclopropyl}-5-fluoropyridine-2-carboxamide
C15 H17 F N4 O2 S
OWWIYTVWTQBRDL-FGAILIKWSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
G [auth A],
N [auth B],
O [auth B]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
L [auth B],
M [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.138 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.548α = 90
b = 90.294β = 90
c = 131.583γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

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: 2019-12-11
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references