PDBsum entry 2nqg

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Hydrolase PDB id
Protein chain
322 a.a. *
_CA ×2
Waters ×126
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Calpain 1 proteolytic core inactivated by wr18(s,s), an epoxysuccinyl-type inhibitor.
Structure: Calpain-1 catalytic subunit. Chain: a. Fragment: calpain catalytic domain, residues 27-356. Synonym: calpain-1 large subunit, calcium-activated neutral proteinase 1, canp 1, calpain mu-type, mucanp, micromolar-calpain. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: capn1, cls1. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
2.04Å     R-factor:   0.184     R-free:   0.251
Authors: D.Cuerrier,P.L.Davies,R.L.Campbell,T.Moldoveanu
Key ref:
D.Cuerrier et al. (2007). Development of calpain-specific inactivators by screening of positional scanning epoxide libraries. J Biol Chem, 282, 9600-9611. PubMed id: 17218315 DOI: 10.1074/jbc.M610372200
31-Oct-06     Release date:   09-Jan-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P97571  (CAN1_RAT) -  Calpain-1 catalytic subunit
713 a.a.
322 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Calpain-1.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Cofactor: Ca(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biological process     proteolysis   1 term 
  Biochemical function     calcium ion binding     2 terms  


DOI no: 10.1074/jbc.M610372200 J Biol Chem 282:9600-9611 (2007)
PubMed id: 17218315  
Development of calpain-specific inactivators by screening of positional scanning epoxide libraries.
D.Cuerrier, T.Moldoveanu, R.L.Campbell, J.Kelly, B.Yoruk, S.H.Verhelst, D.Greenbaum, M.Bogyo, P.L.Davies.
Calpains are calcium-dependent proteases that are required for numerous intracellular processes but also play an important role in the development of pathologies such as ischemic injury and neurodegeneration. Many current small molecule calpain inhibitors also inhibit other cysteine proteases, including cathepsins, and need improved selectivity. The specificity of inhibition of several calpains and papain was profiled using synthetic positional scanning libraries of epoxide-based compounds that target the active-site cysteine. These peptidomimetic libraries probe the P4, P3, and P2 positions, display (S,S)- or (R,R)-epoxide stereochemistries, and incorporate both natural and non-natural amino acids. To facilitate library screening, an SDS-PAGE assay that measures the extent of hydrolysis of an inactive recombinant m-calpain was developed. Individual epoxide inhibitors were synthesized guided by calpain-specific preferences observed from the profiles and tested for inhibition against calpain. The most potent compounds were assayed for specificity against cathepsins B, L, and K. Several compounds demonstrated high inhibition specificity for calpains over cathepsins. The best of these inhibitors, WRH(R,R), irreversibly inactivates m- and mu-calpain rapidly (k(2)/K(i) = 131,000 and 16,500 m(-1) s(-1), respectively) but behaves exclusively as a reversible and less potent inhibitor toward the cathepsins. X-ray crystallography of the proteolytic core of rat mu-calpain inactivated by the epoxide compounds WR gamma-cyano-alpha-aminobutyric acid (S,S) and WR allylglycine (R,R) reveals that the stereochemistry of the epoxide influences positioning and orientation of the P2 residue, facilitating alternate interactions within the S2 pocket. Moreover, the WR gamma-cyano-alpha-aminobutyric acid (S,S)-complexed structure defines a novel hydrogen-bonding site within the S2 pocket of calpains.
  Selected figure(s)  
Figure 7.
FIGURE 7. Crystal structures of µI–II inactivated by WR18(S,S) and WR13(R,R). A and B, fitted electron density of WR18(S,S) and WR13(R,R), respectively. The observed electron density for the ligands is shown by an F[o] – F[c] (omit) map calculated for the structures omitting the ligands and contoured at 2 . C and D, stereo images demonstrating the hydrogen bonds formed by WR18(S,S) and WR13(R,R), respectively. All polar bonds shorter than 3.2 Å are shown by dashes. Carbon atoms of the polypeptide are colored white, and water molecules are shown as red spheres. The flexible P3-Arg and P4-Trp moieties of the ligands were omitted for clarity. Arrows point to the hydrogen bond between WR18(S,S) and a water molecule within the S2 pocket in C and to the (R,R)-epoxide specific hydrogen bond between the P2 backbone amide of WR13(R,R) and Gly-271 in D.
Figure 8.
FIGURE 8. Structural overlap of three epoxide-derived ligands. The overlap of WR18(S,S), WR13(R,R) and E-64 was obtained by the structural alignment of the -carbons of the polypeptide chain. The color scheme is as in Fig. 7, with carbon atoms of E-64 in pink. The active site for the WR18(S,S) complex is shown as a surface. Arrows point to the position of the -carbons of the P2 residues. The flexible P3-Arg and P4-Trp moieties of WR13(R,R) and WR18(S,S) were omitted for clarity.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 9600-9611) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21434837 I.O.Donkor (2011).
Calpain inhibitors: a survey of compounds reported in the patent and scientific literature.
  Expert Opin Ther Pat, 21, 601-636.  
19846712 D.P.Schafer, S.Jha, F.Liu, T.Akella, L.D.McCullough, and M.N.Rasband (2009).
Disruption of the axon initial segment cytoskeleton is a new mechanism for neuronal injury.
  J Neurosci, 29, 13242-13254.  
18627259 C.G.Yu, A.Joshi, and J.W.Geddes (2008).
Intraspinal MDL28170 microinjection improves functional and pathological outcome following spinal cord injury.
  J Neurotrauma, 25, 833-840.  
19278481 H.Y.Lee, J.D.Morton, L.J.Robertson, J.D.McDermott, R.Bickerstaffe, A.D.Abell, M.A.Jones, J.M.Mehrtens, and J.M.Coxon (2008).
Evaluation of a novel calpain inhibitor as a treatment for cataract.
  Clin Experiment Ophthalmol, 36, 852-860.  
19020622 T.Moldoveanu, K.Gehring, and D.R.Green (2008).
Concerted multi-pronged attack by calpastatin to occlude the catalytic cleft of heterodimeric calpains.
  Nature, 456, 404-408.
PDB code: 3df0
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