2G8J

Calpain 1 proteolytic core in complex with SNJ-1945, a alpha-ketoamide-type inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  

  • 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: Capn1 (Cls1)
EC: 3.4.22.52
Find proteins for P97571 (Rattus norvegicus)
Go to UniProtKB:  P97571
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D7G
Query on D7G

Download SDF File 
Download CCD File 
A
((1S)-1-((((1S)-1-BENZYL-3-(CYCLOPROPYLAMINO)-2,3-DIOXOPROPYL)AMINO)CARBONYL)-3-METHYLBUTYL)CARBAMIC ACID 5-METHOXY-3-OXAPENTYL ESTER
SNJ-1945
C25 H37 N3 O7
PMEQLUMDXFJNRY-SFTDATJTSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D7GIC50: 170 nM (87) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.572α = 90.00
b = 70.400β = 90.00
c = 110.895γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
PDB_EXTRACTdata extraction
MOLREPphasing
MAR345data collection
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description