5LU9

Crystal structure of YVAD-cmk bound human legumain (AEP) in complex with compound 11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Inhibition of delta-secretase improves cognitive functions in mouse models of Alzheimer's disease.

Zhang, Z.Obianyo, O.Dall, E.Du, Y.Fu, H.Liu, X.Kang, S.S.Song, M.Yu, S.P.Cabrele, C.Schubert, M.Li, X.Wang, J.Z.Brandstetter, H.Ye, K.

(2017) Nat Commun 8: 14740-14740

  • DOI: 10.1038/ncomms14740
  • Primary Citation of Related Structures:  
    5LU9, 5LU8, 5LUA, 5LUB

  • PubMed Abstract: 
  • δ-secretase, also known as asparagine endopeptidase (AEP) or legumain, is a lysosomal cysteine protease that cleaves both amyloid precursor protein (APP) and tau, mediating the amyloid-β and tau pathology in Alzheimer's disease (AD). Here we report t ...

    δ-secretase, also known as asparagine endopeptidase (AEP) or legumain, is a lysosomal cysteine protease that cleaves both amyloid precursor protein (APP) and tau, mediating the amyloid-β and tau pathology in Alzheimer's disease (AD). Here we report the therapeutic effect of an orally bioactive and brain permeable δ-secretase inhibitor in mouse models of AD. We performed a high-throughput screen and identified a non-toxic and selective δ-secretase inhibitor, termed compound 11, that specifically blocks δ-secretase but not other related cysteine proteases. Co-crystal structure analysis revealed a dual active site-directed and allosteric inhibition mode of this compound class. Chronic treatment of tau P301S and 5XFAD transgenic mice with this inhibitor reduces tau and APP cleavage, ameliorates synapse loss and augments long-term potentiation, resulting in protection of memory. Therefore, these findings demonstrate that this δ-secretase inhibitor may be an effective clinical therapeutic agent towards AD.


    Organizational Affiliation

    Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia 30322, USA.



Macromolecules
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AC-TYR-VAL-ALA-ASP-CHLOROMETHYLKETONEC6synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LegumainA263Homo sapiensMutation(s): 1 
Gene Names: LGMNPRSC1
EC: 3.4.22.34
Find proteins for Q99538 (Homo sapiens)
Explore Q99538 
Go to UniProtKB:  Q99538
NIH Common Fund Data Resources
PHAROS  Q99538
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
3Y7
Query on 3Y7

Download Ideal Coordinates CCD File 
A
7-(morpholin-4-yl)-2,1,3-benzoxadiazol-4-amine
C10 H12 N4 O2
LWCSTSZSZFUHAT-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SNN
Query on SNN
AL-PEPTIDE LINKINGC4 H6 N2 O2ASN
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 1
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002086
Query on PRD_002086
CACE-TYR-VAL-ALA-ASP-CHLOROMETHYLKETONEPeptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 
  • Space Group: P 42
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.39α = 90
b = 64.39β = 90
c = 79.33γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Database references
  • Version 1.2: 2018-06-13
    Changes: Data collection, Structure summary
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary