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 4FGX | pdb_00004fgx

Crystal structure of bace1 with novel inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 
    0.181 (Depositor), 0.178 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4FGX

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

Literature

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

(2012) J Med Chem 55: 10749-10765

  • DOI: https://doi.org/10.1021/jm301630s
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 49.55 kDa 
  • Atom Count: 3,472 
  • Modeled Residue Count: 382 
  • Deposited Residue Count: 440 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-secretase 1433Homo 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
GTEx:  ENSG00000186318 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Inhibitor (2R,5S,8S,12S,13S,16S,19S,22S)-16-(3-amino-3-oxopropyl)-2,13-dibenzyl-12,22-dihydroxy-8-isobutyl-19-isopropyl-3,5,17-trimethyl-4,7,10,15,18,21-hexaoxo-3,6,9,14,17,20-hexaazatricosan-1-oic acid7N/AMutation(s): 0 
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free:  0.181 (Depositor), 0.178 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.71α = 90
b = 128.73β = 90
c = 76.16γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



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: Advisory, Database references, Derived calculations