4WQ2

Human calpain PEF(S) with (Z)-3-(6-bromondol-3-yl)-2-mercaptoacrylic acid bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report



Literature

Conformationally restricted calpain inhibitors.

Adams, S.E.Robinson, E.J.Miller, D.J.Rizkallah, P.J.Hallett, M.B.Allemann, R.K.

(2015) Chem Sci 6: 6865-6871

  • DOI: 10.1039/c5sc01158b
  • Primary Citation of Related Structures:  
    5D69, 4WQ2, 4WQ3

  • PubMed Abstract: 
  • The cysteine protease calpain-I is linked to several diseases and is therefore a valuable target for inhibition. Selective inhibition of calpain-I has proved difficult as most compounds target the active site and inhibit a broad spectrum of cysteine prot ...

    The cysteine protease calpain-I is linked to several diseases and is therefore a valuable target for inhibition. Selective inhibition of calpain-I has proved difficult as most compounds target the active site and inhibit a broad spectrum of cysteine proteases as well as other calpain isoforms. Selective inhibitors might not only be potential drugs but should act as tools to explore the physiological and pathophysiological roles of calpain-I. α-Mercaptoacrylic acid based calpain inhibitors are potent, cell permeable and selective inhibitors of calpain-I and calpain-II. These inhibitors target the calcium binding domain PEF(S) of calpain-I and -II. Here X-ray diffraction analysis of co-crystals of PEF(S) revealed that the disulfide form of an α-mercaptoacrylic acid bound within a hydrophobic groove that is also targeted by a calpastatin inhibitory region and made a greater number of favourable interactions with the protein than the reduced sulfhydryl form. Measurement of the inhibitory potency of the α-mercaptoacrylic acids and X-ray crystallography revealed that the IC 50 values decreased significantly on oxidation as a consequence of the stereo-electronic properties of disulfide bonds that restrict rotation around the S-S bond. Consequently, thioether analogues inhibited calpain-I with potencies similar to those of the free sulfhydryl forms of α-mercaptoacrylic acids.


    Organizational Affiliation

    School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , UK CF10 3AT . Email: allemannrk@cardiff.ac.uk ; ; Tel: +44 (0) 29 2087 9014.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Calpain small subunit 1 AB173Homo sapiensMutation(s): 0 
Gene Names: CAPNS1CAPN4CAPNS
Find proteins for P04632 (Homo sapiens)
Explore P04632 
Go to UniProtKB:  P04632
NIH Common Fund Data Resources
PHAROS:  P04632
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.72α = 90
b = 78.43β = 91.12
c = 56.3γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
Cootmodel building
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomG0701192

Revision History 

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Database references
  • Version 2.0: 2017-09-13
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations