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

Experimental Data Snapshot

  • 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

Ligand Structure Quality Assessment 

This is version 2.1 of the entry. See complete history


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: https://doi.org/10.1039/c5sc01158b
  • Primary Citation of Related Structures:  
    4WQ2, 4WQ3, 5D69

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calpain small subunit 1
A, B
173Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P04632 (Homo sapiens)
Explore P04632 
Go to UniProtKB:  P04632
PHAROS:  P04632
GTEx:  ENSG00000126247 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04632
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 3SU

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
(2Z)-3-(6-bromo-1H-indol-3-yl)-2-sulfanylprop-2-enoic acid
C11 H8 Br N O2 S
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
O [auth B],
P [auth B]
C2 H6 O2
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
K [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
Experimental Data & Validation

Experimental Data

  • 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
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • 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
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description