7RNF

Crystal structure of caspase-3 with inhibitor Ac-VDKVD-CHO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 3.1 of the entry. See complete history


Literature

Structure-Based Design and Biological Evaluation of Novel Caspase-2 Inhibitors Based on the Peptide AcVDVAD-CHO and the Caspase-2-Mediated Tau Cleavage Sequence YKPVD314.

Bresinsky, M.Strasser, J.M.Vallaster, B.Liu, P.McCue, W.M.Fuller, J.Hubmann, A.Singh, G.Nelson, K.M.Cuellar, M.E.Wilmot, C.M.Finzel, B.C.Ashe, K.H.Walters, M.A.Pockes, S.

(2022) Acs Pharmacol Transl Sci 5: 20-40

  • DOI: https://doi.org/10.1021/acsptsci.1c00251
  • Primary Citation of Related Structures:  
    7RN7, 7RN8, 7RN9, 7RNB, 7RND, 7RNE, 7RNF, 7SEO

  • PubMed Abstract: 

    Alzheimer's disease (AD) was first described by Alois Alzheimer over 100 years ago, but there is still no overarching theory that can explain its cause in detail. There are also no effective therapies to treat either the cause or the associated symptoms of this devastating disease. A potential approach to better understand the pathogenesis of AD could be the development of selective caspase-2 (Casp2) probes, as we have shown that a Casp2-mediated cleavage product of tau (Δtau314) reversibly impairs cognitive and synaptic function in animal models of tauopathies. In this article, we map out the Casp2 binding site through the preparation and assay of a series of 35 pentapeptide inhibitors with the goal of gaining selectivity against caspase-3 (Casp3). We also employed computational docking methods to understand the key interactions in the binding pocket of Casp2 and the differences predicted for binding at Casp3. Moreover, we crystallographically characterized the binding of selected pentapeptides with Casp3. Furthermore, we engineered and expressed a series of recombinant tau mutants and investigated them in an in vitro cleavage assay. These studies resulted in simple peptidic inhibitors with nanomolar affinity, for example, AcVDV(Dab)D-CHO ( 24 ) with up to 27.7-fold selectivity against Casp3. Our findings provide a good basis for the future development of selective Casp2 probes and inhibitors that can serve as pharmacological tools in planned in vivo studies and as lead compounds for the design of bioavailable and more drug-like small molecules.


  • Organizational Affiliation

    Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, Regensburg 93053, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-3 subunit p17
A, C
141Homo sapiensMutation(s): 0 
Gene Names: CASP3CPP32
EC: 3.4.22.56
UniProt & NIH Common Fund Data Resources
Find proteins for P42574 (Homo sapiens)
Explore P42574 
Go to UniProtKB:  P42574
PHAROS:  P42574
GTEx:  ENSG00000164305 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42574
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-3 subunit p12
B, D
95Homo sapiensMutation(s): 0 
Gene Names: CASP3CPP32
EC: 3.4.22.56
UniProt & NIH Common Fund Data Resources
Find proteins for P42574 (Homo sapiens)
Explore P42574 
Go to UniProtKB:  P42574
PHAROS:  P42574
GTEx:  ENSG00000164305 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42574
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ac-VDKVD-CHOE [auth F],
F [auth G]
6synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ASA
Query on ASA
E [auth F],
F [auth G]
L-PEPTIDE LINKINGC4 H7 N O3ASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.34α = 90
b = 67.081β = 91.137
c = 82.183γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
AutoProcessdata reduction
PHASERphasing
JDirectordata collection

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United States5R01AG062199-03

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-05
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Database references
  • Version 2.0: 2023-06-28
    Changes: Advisory, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 3.0: 2024-02-07
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary
  • Version 3.1: 2024-11-13
    Changes: Structure summary