4N7M

Tailoring Small Molecules for an Allosteric Site on Procaspase-6

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Tailoring small molecules for an allosteric site on procaspase-6.

Murray, J., Giannetti, A.M., Steffek, M., Gibbons, P., Hearn, B.R., Cohen, F., Tam, C., Pozniak, C., Bravo, B., Lewcock, J., Jaishankar, P., Ly, C.Q., Zhao, X., Tang, Y., Chugha, P., Arkin, M.R., Flygare, J., Renslo, A.R.

(2014) ChemMedChem 9: 73-77

  • DOI: 10.1002/cmdc.201300424
  • Primary Citation of Related Structures:  
    4N5D, 4N6G, 4N7M, 4N7J, 4NBK, 4NBL, 4NBN

  • PubMed Abstract: 

    • Although they represent attractive therapeutic targets, caspases have so far proven recalcitrant to the development of drugs targeting the active site. Allosteric modulation of caspase activity is an alternate strategy that potentially avoids the need for anionic and electrophilic functionality present in most active-site inhibitors ...

    Although they represent attractive therapeutic targets, caspases have so far proven recalcitrant to the development of drugs targeting the active site. Allosteric modulation of caspase activity is an alternate strategy that potentially avoids the need for anionic and electrophilic functionality present in most active-site inhibitors. Caspase-6 has been implicated in neurodegenerative disease, including Huntington's and Alzheimer's diseases. Herein we describe a fragment-based lead discovery effort focused on caspase-6 in its active and zymogen forms. Fragments were identified for procaspase-6 using surface plasmon resonance methods and subsequently shown by X-ray crystallography to bind a putative allosteric site at the dimer interface. A fragment-merging strategy was employed to produce nanomolar-affinity ligands that contact residues in the L2 loop at the dimer interface, significantly stabilizing procaspase-6. Because rearrangement of the L2 loop is required for caspase-6 activation, our results suggest a strategy for the allosteric control of caspase activation with drug-like small molecules.

    Organizational Affiliation: 

    Departments of Structural Biology, Biochemical Pharmacology, Neuroscience, and Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080 (USA). murray.jeremy@gene.com.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Caspase-6 A, B282Homo sapiensMutation(s): 1 
Gene Names: CASP6, MCH2, procaspase-6
EC: 3.4.22.59
Find proteins for P55212 (Homo sapiens)
Explore P55212 
Go to UniProtKB:  P55212
NIH Common Fund Data Resources
PHAROS:  P55212
GTEx:  ENSG00000138794
Protein Feature View
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  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2GQKd :  3400   nM  PDBBind
2GQKd:  3400   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.7α = 90
b = 115.7β = 90
c = 79.691γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
XSCALEdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2014-01-22
    Changes: Database references
  • Version 1.2: 2014-12-10
    Changes: Structure summary