3RJM

CASPASE2 IN COMPLEX WITH CHDI LIGAND 33c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Exploiting differences in caspase-2 and -3 S(2) subsites for selectivity: Structure-based design, solid-phase synthesis and in vitro activity of novel substrate-based caspase-2 inhibitors.

Maillard, M.C.Brookfield, F.A.Courtney, S.M.Eustache, F.M.Gemkow, M.J.Handel, R.K.Johnson, L.C.Johnson, P.D.Kerry, M.A.Krieger, F.Meniconi, M.Munoz-Sanjuan, I.Palfrey, J.J.Park, H.Schaertl, S.Taylor, M.G.Weddell, D.Dominguez, C.

(2011) Bioorg.Med.Chem. 19: 5833-5851

  • DOI: 10.1016/j.bmc.2011.08.020

  • PubMed Abstract: 
  • Several caspases have been implicated in the pathogenesis of Huntington's disease (HD); however, existing caspase inhibitors lack the selectivity required to investigate the specific involvement of individual caspases in the neuronal cell death assoc ...

    Several caspases have been implicated in the pathogenesis of Huntington's disease (HD); however, existing caspase inhibitors lack the selectivity required to investigate the specific involvement of individual caspases in the neuronal cell death associated with HD. In order to explore the potential role played by caspase-2, the potent but non-selective canonical Ac-VDVAD-CHO caspase-2 inhibitor 1 was rationally modified at the P(2) residue in an attempt to decrease its activity against caspase-3. With the aid of structural information on the caspase-2, and -3 active sites and molecular modeling, a 3-(S)-substituted-l-proline along with four additional scaffold variants were selected as P(2) elements for their predicted ability to clash sterically with a residue of the caspase-3 S(2) pocket. These elements were then incorporated by solid-phase synthesis into pentapeptide aldehydes 33a-v. Proline-based compound 33h bearing a bulky 3-(S)-substituent displayed advantageous characteristics in biochemical and cellular assays with 20- to 60-fold increased selectivity for caspase-2 and ∼200-fold decreased caspase-3 potency compared to the reference inhibitor 1. Further optimization of this prototype compound may lead to the discovery of valuable pharmacological tools for the study of caspase-2 mediated cell death, particularly as it relates to HD.


    Organizational Affiliation

    CHDI Management, Inc., 6080 Center Drive Suite 100, Los Angeles, CA 90045, USA. michel.maillard@chdifoundation.org




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Caspase-2
A, C
169Homo sapiensMutation(s): 0 
Gene Names: CASP2 (ICH1, NEDD2)
EC: 3.4.22.55
Find proteins for P42575 (Homo sapiens)
Go to Gene View: CASP2
Go to UniProtKB:  P42575
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Caspase-2
B, D
117Homo sapiensMutation(s): 0 
Gene Names: CASP2 (ICH1, NEDD2)
EC: 3.4.22.55
Find proteins for P42575 (Homo sapiens)
Go to Gene View: CASP2
Go to UniProtKB:  P42575
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Peptide inhibitor (ACE)VDV(3PX)D-CHO
E, F
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000786
Query on PRD_000786
E,FPeptide inhibitor (ACE)VDV(3PX)D-CHOPeptide-like / CASPASE inhibitor

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.770α = 90.00
b = 97.380β = 90.00
c = 97.980γ = 90.00
Software Package:
Software NamePurpose
StructureStudiodata collection
XDSdata reduction
REFMACrefinement
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2011-10-05
    Type: Database references
  • Version 1.2: 2012-12-12
    Type: Other