6DEU

Human caspase-6 A109T


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.796 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.267 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Identification of Allosteric Inhibitors against Active Caspase-6.

Tubeleviciute-Aydin, A.Beautrait, A.Lynham, J.Sharma, G.Gorelik, A.Deny, L.J.Soya, N.Lukacs, G.L.Nagar, B.Marinier, A.LeBlanc, A.C.

(2019) Sci Rep 9: 5504-5504

  • DOI: 10.1038/s41598-019-41930-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Caspase-6 is a cysteine protease that plays essential roles in programmed cell death, axonal degeneration, and development. The excess neuronal activity of Caspase-6 is associated with Alzheimer disease neuropathology and age-dependent cognitive impa ...

    Caspase-6 is a cysteine protease that plays essential roles in programmed cell death, axonal degeneration, and development. The excess neuronal activity of Caspase-6 is associated with Alzheimer disease neuropathology and age-dependent cognitive impairment. Caspase-6 inhibition is a promising strategy to stop early stage neurodegenerative events, yet finding potent and selective Caspase-6 inhibitors has been a challenging task due to the overlapping structural and functional similarities between caspase family members. Here, we investigated how four rare non-synonymous missense single-nucleotide polymorphisms (SNPs), resulting in amino acid substitutions outside human Caspase-6 active site, affect enzyme structure and catalytic efficiency. Three investigated SNPs were found to align with a putative allosteric pocket with low sequence conservation among human caspases. Virtual screening of 57,700 compounds against the putative Caspase-6 allosteric pocket, followed by in vitro testing of the best virtual hits in recombinant human Caspase-6 activity assays identified novel allosteric Caspase-6 inhibitors with IC 50 and K i values ranging from ~2 to 13 µM. This report may pave the way towards the development and optimisation of novel small molecule allosteric Caspase-6 inhibitors and illustrates that functional characterisation of rare natural variants holds promise for the identification of allosteric sites on other therapeutic targets in drug discovery.


    Organizational Affiliation

    Department of Anatomy and Cell Biology, McGill University, 3640 University St., Montreal, Quebec, H3A 0C7, Canada. andrea.leblanc@mcgill.ca.,Department of Biochemistry, McGill University, 3649 promenade Sir-William-Osler, Montreal, Quebec, H3G 0B1, Canada.,Institute for Research in Immunology and Cancer, Université de Montréal, 2590, chemin de Polytechnique, Montreal, Quebec, H3T 1J4, Canada.,Bloomfield Center for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Ch. Cote Ste-Catherine, Montreal, Quebec, H3T 1E2, Canada. andrea.leblanc@mcgill.ca.,Department of Neurology and Neurosurgery, McGill University, 3775 University St., Montreal, Quebec, H3A 2B4, Canada.,Department of Physiology and Biochemistry, McGill University, 3655 Promenade Sir-William-Osler, Montréal, Québec, H3G 1Y6, Canada.,Bloomfield Center for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Ch. Cote Ste-Catherine, Montreal, Quebec, H3T 1E2, Canada.,Department of Anatomy and Cell Biology, McGill University, 3640 University St., Montreal, Quebec, H3A 0C7, Canada.,Department of Neurology and Neurosurgery, McGill University, 3775 University St., Montreal, Quebec, H3A 2B4, Canada. andrea.leblanc@mcgill.ca.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Caspase-6
A, B
302Homo sapiensMutation(s): 1 
Gene Names: CASP6 (MCH2)
EC: 3.4.22.59
Find proteins for P55212 (Homo sapiens)
Go to Gene View: CASP6
Go to UniProtKB:  P55212
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.796 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.267 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 91.113α = 90.00
b = 63.929β = 90.00
c = 86.534γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP-243413-BCA-CGAG-45097

Revision History 

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-04-17
    Type: Data collection, Database references
  • Version 1.2: 2020-01-08
    Type: Author supporting evidence