2G8E

Calpain 1 proteolytic core in complex with SNJ-1715, a cyclic hemiacetal-type inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Calpain Inhibition by alpha-Ketoamide and Cyclic Hemiacetal Inhibitors Revealed by X-ray Crystallography

Cuerrier, D.Moldoveanu, T.Inoue, J.Davies, P.L.Campbell, R.L.

(2006) Biochemistry 45: 7446-7452

  • DOI: 10.1021/bi060425j
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Calpains are intracellular calcium-activated cysteine proteases whose unregulated proteolysis following the loss of calcium homeostasis can lead to acute degeneration during ischemic episodes and trauma, as well as Alzheimer's disease and cataract fo ...

    Calpains are intracellular calcium-activated cysteine proteases whose unregulated proteolysis following the loss of calcium homeostasis can lead to acute degeneration during ischemic episodes and trauma, as well as Alzheimer's disease and cataract formation. The determination of the crystal structure of the proteolytic core of mu-calpain (muI-II) in a calcium-bound active conformation has made structure-guided design of active site inhibitors feasible. We present here high-resolution crystal structures of rat muI-II complexed with two reversible calpain-specific inhibitors employing cyclic hemiacetal (SNJ-1715) and alpha-ketoamide (SNJ-1945) chemistries that reveal new details about the interactions of inhibitors with this enzyme. The SNJ-1715 complex confirms that the free aldehyde is the reactive species of the cornea-permeable cyclic hemiacetal. The alpha-ketoamide warhead of SNJ-1945 binds with the hydroxyl group of the tetrahedral adduct pointing toward the catalytic histidine rather than the oxyanion hole. The muI-II-SNJ-1945 complex shows residue Glu261 displaced from the S1' site by the inhibitor, resulting in an extended "open" conformation of the domain II gating loop and an unobstructed S1' site. This conformation offers an additional template for structure-based drug design extending to the primed subsites. An important role for the highly conserved Glu261 is proposed.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Calpain-1 catalytic subunit
A
339Rattus norvegicusMutation(s): 0 
Gene Names: Capn1Cls1
EC: 3.4.22.52
Find proteins for P97571 (Rattus norvegicus)
Go to UniProtKB:  P97571
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0M6
Query on 0M6

Download CCD File 
A
N-[(2S)-1,4-dihydroxybutan-2-yl]-N~2~-(phenylcarbamothioyl)-L-leucinamide
C17 H27 N3 O3 S
OXLJDYBAHYSQNA-GJZGRUSLSA-N
 Ligand Interaction
MES
Query on MES

Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.181 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.542α = 90
b = 85.542β = 90
c = 117.946γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-03-14
    Changes: Non-polymer description, Structure summary
  • Version 1.4: 2017-10-18
    Changes: Refinement description