5D69

Human calpain PEF(S) with (2Z,2Z')-2,2'-disulfanediylbis(3-(6-iodoindol-3-yl)acrylic acid) bound

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


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 A, B173Homo sapiensMutation(s): 0 
Gene Names: CAPNS1, CAPN4, CAPNS
Find proteins for P04632 (Homo sapiens)
Explore P04632 
Go to UniProtKB:  P04632
NIH Common Fund Data Resources
PHAROS:  P04632
GTEx:  ENSG00000126247
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.03α = 90
b = 79.65β = 91.81
c = 57.16γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
xia2data reduction

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
EPSRC and MRCUnited KingdomG0701192

Revision History 

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2017-08-16
    Changes: Database references