Crystal structure of BACE1 with its inhibitor

Experimental Data Snapshot

  • Resolution: 2.08 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

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Cyanobacterial Peptides as a Prototype for the Design of Potent beta-Secretase Inhibitors and the Development of Selective Chemical Probes for Other Aspartic Proteases

Liu, Y.Zhang, W.Li, L.Salvador, L.A.Chen, T.T.Chen, W.Y.Felsenstein, K.M.Ladd, T.B.Price, A.R.Golde, T.E.He, J.Xu, Y.C.Li, Y.Luesch, H.

(2012) J Med Chem 55: 10749-10765

  • DOI: https://doi.org/10.1021/jm301630s
  • Primary Citation of Related Structures:  
    3UQP, 3UQR, 4DV9, 4DVF, 4FGX

  • PubMed Abstract: 

    Inspired by marine cyanobacterial natural products, we synthesized modified peptides with a central statine-core unit, characteristic for aspartic protease inhibition. A series of tasiamide B analogues inhibited BACE1, a therapeutic target in Alzheimer's disease. We probed the stereospecificity of target engagement and determined additional structure-activity relationships with respect to BACE1 and related aspartic proteases, cathepsins D and E. We cocrystallized selected inhibitors with BACE1 to reveal the structural basis for the activity. Hybrid molecules that combine features of tasiamide B and an isophthalic acid moiety-containing sulfonamide showed nanomolar cellular activity. Compounds were screened in a series of rigorous complementary cell-based assays. We measured secreted APP ectodomain (sAPPβ), membrane bound carboxyl terminal fragment (CTF), levels of β-amyloid (Aβ) peptides and selectivity for β-secretase (BACE1) over γ-secretase. Prioritized compounds showed reasonable stability in vitro and in vivo, and our most potent inhibitor showed efficacy in reducing Aβ levels in the rodent brain.

  • Organizational Affiliation

    Department of Medicinal Chemistry, University of Florida, Gainesville, Florida 32610, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1433Homo sapiensMutation(s): 2 
Gene Names: BACE1
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
PHAROS:  P56817
GTEx:  ENSG00000186318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
METHYL (2S)-1-[(2R,5S,8S,12S,13S,16S,19S,22S)-16-(3-AMINO-3-OXOPROPYL)-2,13-DIBENZYL-12,22-DIHYDROXY-3,5,17-TRIMETHYL-8-(2-METHYLPROPYL)-4,7,10,15,18,21-HEXAOXO-19-(PROPAN-2-YL)-3,6,9,14,17,20-HEXAAZATRICOSAN-1-OYL]PYRROLIDINE-2-CARBOXYLATE (NON-PREFERRED NAME)8synthetic constructMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.08 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.528α = 90
b = 128.846β = 90
c = 76.766γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2021-09-15
    Changes: Database references, Derived calculations, Source and taxonomy