6DEV | pdb_00006dev

Human caspase-6 E35K

• PDB DOI: https://doi.org/10.2210/pdb6DEV/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-05-13 Released: 2019-03-27 
• Deposition Author(s): 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.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.248 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

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

• PubMed: 30940883 
• DOI: https://doi.org/10.1038/s41598-019-41930-7
• Primary Citation Related Structures: 
  6DEU, 6DEV


• 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 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.

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Organizational Affiliation: 
• 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 Neurology and Neurosurgery, McGill University, 3775 University St., Montreal, Quebec, H3A 2B4, Canada.
Institute for Research in Immunology and Cancer, Université de Montréal, 2590, chemin de Polytechnique, Montreal, Quebec, H3T 1J4, Canada.
Department of Anatomy and Cell Biology, McGill University, 3640 University St., Montreal, Quebec, H3A 0C7, Canada.
Department of Biochemistry, McGill University, 3649 promenade Sir-William-Osler, Montreal, Quebec, H3G 0B1, 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. [e-mail].
Department of Neurology and Neurosurgery, McGill University, 3775 University St., Montreal, Quebec, H3A 2B4, Canada. [e-mail].
Department of Anatomy and Cell Biology, McGill University, 3640 University St., Montreal, Quebec, H3A 0C7, Canada. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 138.01 kDa 
• Atom Count: 7,425 
• Modeled Residue Count: 898 
• Deposited Residue Count: 1,208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-6	A, B, C, D	302	Homo sapiens	Mutation(s): 1  Gene Names: CASP6, MCH2 EC: 3.4.22.59
UniProt & NIH Common Fund Data Resources
Find proteins for P55212 (Homo sapiens) Explore P55212  Go to UniProtKB:  P55212
PHAROS:  P55212 GTEx:  ENSG00000138794

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.248 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.385	α = 90
b = 91.326	β = 91.8
c = 86.682	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	MOP-243413-BCA-CGAG-45097

Revision History  

• Version 1.0: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Data collection, Database references
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description