4K9H

Bace-1 inhibitor complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

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Ligand Structure Quality Assessment 


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Literature

Hydroxyethylamine-based inhibitors of BACE1: P1-P3 macrocyclization can improve potency, selectivity, and cell activity.

Pennington, L.D., Whittington, D.A., Bartberger, M.D., Jordan, S.R., Monenschein, H., Nguyen, T.T., Yang, B.H., Xue, Q.M., Vounatsos, F., Wahl, R.C., Chen, K., Wood, S., Citron, M., Patel, V.F., Hitchcock, S.A., Zhong, W.

(2013) Bioorg Med Chem Lett 23: 4459-4464

  • DOI: https://doi.org/10.1016/j.bmcl.2013.05.028
  • Primary Citation of Related Structures:  
    4K8S, 4K9H, 4KE0, 4KE1

  • PubMed Abstract: 

    • We describe a systematic study of how macrocyclization in the P₁-P₃ region of hydroxyethylamine-based inhibitors of β-site amyloid precursor protein (APP)-cleaving enzyme (BACE1) modulates in vitro activity. This study reveals that in a number of instances macrocyclization of bis-terminal dienes leads to improved potency toward BACE1 and selectivity against cathepsin D (CatD), as well as greater amyloid β-peptide (Aβ)-lowering activity in HEK293T cells stably expressing APPSW ...

    We describe a systematic study of how macrocyclization in the P₁-P₃ region of hydroxyethylamine-based inhibitors of β-site amyloid precursor protein (APP)-cleaving enzyme (BACE1) modulates in vitro activity. This study reveals that in a number of instances macrocyclization of bis-terminal dienes leads to improved potency toward BACE1 and selectivity against cathepsin D (CatD), as well as greater amyloid β-peptide (Aβ)-lowering activity in HEK293T cells stably expressing APPSW. However, for several closely related analogs the benefits of macrocyclization are attenuated by the effects of other structural features in different regions of the molecules. X-ray crystal structures of three of these novel macrocyclic inhibitors bound to BACE1 revealed their binding conformations and interactions with the enzyme.

    Organizational Affiliation: 

    Medicinal Chemistry, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA. lewpenn@icloud.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1
A, B, C
388Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1QU
Query on 1QU
Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]		1-cyclopentyl-N-[(2S,3R)-3-hydroxy-1-phenyl-4-{[3-(trifluoromethyl)benzyl]amino}butan-2-yl]-6-oxo-5-(2-oxopyrrolidin-1-yl)-1,6-dihydropyridine-3-carboxamide
C33 H37 F3 N4 O4
QKLJNYJRYSKKKP-LMSSTIIKSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1QU Binding MOAD:  4K9H IC50: 76 (nM) from 1 assay(s)
PDBBind:  4K9H IC50: 76 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.538α = 90
b = 103.304β = 104.01
c = 100.856γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
X-PLORmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2013-07-10 
    • Deposition Author(s): Jordan, S.R.

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references