2R9F

Calpain 1 proteolytic core inactivated by ZLAK-3002, an alpha-ketoamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cocrystal structures of primed side-extending alpha-ketoamide inhibitors reveal novel calpain-inhibitor aromatic interactions.

Qian, J.Cuerrier, D.Davies, P.L.Li, Z.Powers, J.C.Campbell, R.L.

(2008) J.Med.Chem. 51: 5264-5270

  • DOI: 10.1021/jm800045t
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Calpains are intracellular cysteine proteases that catalyze the cleavage of target proteins in response to Ca(2+) signaling. When Ca(2+) homeostasis is disrupted, calpain overactivation causes unregulated proteolysis, which can contribute to diseases ...

    Calpains are intracellular cysteine proteases that catalyze the cleavage of target proteins in response to Ca(2+) signaling. When Ca(2+) homeostasis is disrupted, calpain overactivation causes unregulated proteolysis, which can contribute to diseases such as postischemic injury and cataract formation. Potent calpain inhibitors exist, but of these many cross-react with other cysteine proteases and will need modification to specifically target calpain. Here, we present crystal structures of rat calpain 1 protease core (muI-II) bound to two alpha-ketoamide-based calpain inhibitors containing adenyl and piperazyl primed-side extensions. An unexpected aromatic-stacking interaction is observed between the primed-side adenine moiety and the Trp298 side chain. This interaction increased the potency of the inhibitor toward muI-II and heterodimeric m-calpain. Moreover, stacking orients the adenine such that it can be used as a scaffold for designing novel primed-side address regions, which could be incorporated into future inhibitors to enhance their calpain specificity.


    Organizational Affiliation

    Department of Biochemistry, Queen's University, Kingston, Ontario, K7L 3N6, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Calpain-1 catalytic subunit
A
339Rattus norvegicusMutation(s): 0 
Gene Names: Capn1 (Cls1)
EC: 3.4.22.52
Find proteins for P97571 (Rattus norvegicus)
Go to UniProtKB:  P97571
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
K2Z
Query on K2Z

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Download CCD File 
A
benzyl [(1S)-1-{[(1S,2S)-1-ethyl-2-hydroxy-3-{[3-(4-methylpiperazin-1-yl)propyl]amino}-3-oxopropyl]carbamoyl}-3-methylbutyl]carbamate
C27 H45 N5 O5
SVPVAMXCDQANIT-HJOGWXRNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.569α = 90.00
b = 70.568β = 90.00
c = 110.406γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
MOLREPphasing
SCALAdata scaling
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Advisory, Refinement description