3QI1

Design and synthesis of hydroxyethylamine (hea) BACE-1 inhibitors: prime side chromane-containing inhibitors

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.202 

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Ligand Structure Quality Assessment 


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Literature

Design and synthesis of hydroxyethylamine (HEA) BACE-1 inhibitors: prime side chromane-containing inhibitors.

Ng, R.A., Sun, M., Bowers, S., Hom, R.K., Probst, G.D., John, V., Fang, L.Y., Maillard, M., Gailunas, A., Brogley, L., Neitz, R.J., Tung, J.S., Pleiss, M.A., Konradi, A.W., Sham, H.L., Dappen, M.S., Adler, M., Yao, N., Zmolek, W., Nakamura, D., Quinn, K.P., Sauer, J.M., Bova, M.P., Ruslim, L., Artis, D.R., Yednock, T.A.

(2013) Bioorg Med Chem Lett 23: 4674-4679

  • DOI: https://doi.org/10.1016/j.bmcl.2013.06.006
  • Primary Citation of Related Structures:  
    3QI1

  • PubMed Abstract: 

    • The structure activity relationship of the prime region of conformationally restricted hydroxyethylamine (HEA) BACE inhibitors is described. Variation of the P1' region provided selectivity over Cat-D with a series of 2,2-dioxo-isothiochromanes and optimization of the P2' substituent of chromane-HEA(s) with polar substituents provided improvements in the compound's in vitro permeability ...

    The structure activity relationship of the prime region of conformationally restricted hydroxyethylamine (HEA) BACE inhibitors is described. Variation of the P1' region provided selectivity over Cat-D with a series of 2,2-dioxo-isothiochromanes and optimization of the P2' substituent of chromane-HEA(s) with polar substituents provided improvements in the compound's in vitro permeability. Significant potency gains were observed with small aliphatic substituents such as methyl, n-propyl, and cyclopropyl when placed at the C-2 position of the chromane.

    Organizational Affiliation: 

    Department of Chemical Sciences, Elan Pharmaceuticals, 180 Oyster Point Boulevard, South San Francisco, CA 94080, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1408Homo sapiensMutation(s): 2 
Gene Names: BACE, BACE1, 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C6A
Query on C6A
Download Ideal Coordinates CCD File 
B [auth A]N-[(2S,3R)-4-{[(2R,4S)-2-cyclopropyl-6-(2,2-dimethylpropyl)-3,4-dihydro-2H-chromen-4-yl]amino}-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]acetamide
C29 H38 F2 N2 O3
IBLLHMQPQAMFLM-WDTRASESSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
C6A PDBBind:  3QI1 IC50: 22 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.174α = 90
b = 75.506β = 90
c = 80.236γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2012-03-28 
    • Deposition Author(s): Yao, N.

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-28
    Type: Initial release
  • Version 1.1: 2013-12-18
    Changes: Database references