Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41670.35 
• Atom Count: 2942 
• Residue Count: 346 
• Unique protein chains: 1

5D69

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

• DOI: 10.2210/pdb5D69/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2015-08-11 Released: 2015-09-02 
• Deposition Author(s): Adams, S.E., Robinson, E.J., Rizkallah, P.J., Miller, D.J., Hallett, M.B., Allemann, R.K.
• Funding Organization(s): EPSRC and MRC 

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Experimental Data Snapshot

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

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

• PubMed: 28757975 
• DOI: 10.1039/c5sc01158b
• Primary Citation of Related Structures:  
  4WQ3, 4WQ2


• 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 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.

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Organizational Affiliation: 

School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff , UK CF10 3AT . Email: [e-mail] ; ; Tel: [phone].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Calpain small subunit 1	A, B	173	Homo sapiens	Mutation(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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
57T	A, B	(2E,2'Z)-2,2'-disulfanediylbis[3-(4-iodophenyl)prop-2-enoic acid] C18 H12 I2 O4 S2 RLKZEUBAGNQDNM-CKOAPEAFSA-N
SO4	B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.234 
• R-Value Work: 0.199 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 50.030	α = 90.00
b = 79.650	β = 91.81
c = 57.160	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
xia2	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-08-11 
• Released Date: 2015-09-02 
• Deposition Author(s): Adams, S.E., Robinson, E.J., Rizkallah, P.J., Miller, D.J., Hallett, M.B., Allemann, R.K.

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Funding Organization	Location	Grant Number
EPSRC and MRC	United Kingdom	G0701192

Revision History 

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