4WQ3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 2.0 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:  

  • 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 ...

    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 IC50 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Calpain small subunit 1
A, B
173Homo sapiensMutation(s): 0 
Gene Names: CAPNS1 (CAPN4, CAPNS)
Find proteins for P04632 (Homo sapiens)
Go to Gene View: CAPNS1
Go to UniProtKB:  P04632
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
3SU
Query on 3SU

Download SDF File 
Download CCD File 
A, B
(2Z)-3-(6-bromo-1H-indol-3-yl)-2-sulfanylprop-2-enoic acid
C11 H8 Br N O2 S
BTHAZQKLFQMXOX-KMKOMSMNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 49.560α = 90.00
b = 79.310β = 91.47
c = 57.020γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PHASERphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling
xia2data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references
  • Version 2.0: 2017-09-13
    Type: Advisory, Atomic model, Author supporting evidence, Derived calculations