Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 65.89 kDa 
• Atom Count: 4307 
• Residue Count: 525 
• Unique protein chains: 3

3RJM

CASPASE2 IN COMPLEX WITH CHDI LIGAND 33c

• DOI: 10.2210/pdb3RJM/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-04-15 Released: 2011-09-21 
• Deposition Author(s): Abendroth, J., Lorimer, D., Stewart, L., Maillard, M., Kiselyov, A.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.249 
• R-Value Work: 0.186 
• R-Value Observed: 0.190 

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

• PubMed: 21903398 
• DOI: 10.1016/j.bmc.2011.08.020
• Primary Citation of Related Structures:  
  3RJM


• 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 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.

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Organizational Affiliation: 

CHDI Management, Inc., 6080 Center Drive Suite 100, Los Angeles, CA 90045, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-2	A, C	169	Homo sapiens	Mutation(s): 0  Gene Names: CASP2, Caspase-2, ICH1, NEDD2, p19 EC: 3.4.22.55
Find proteins for P42575 (Homo sapiens) Explore P42575  Go to UniProtKB:  P42575
NIH Common Fund Data Resources
PHAROS:  P42575 GTEx:  ENSG00000106144

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-2	B, D	117	Homo sapiens	Mutation(s): 0  Gene Names: CASP2, Caspase-2, ICH1, NEDD2, p12 EC: 3.4.22.55
Find proteins for P42575 (Homo sapiens) Explore P42575  Go to UniProtKB:  P42575
NIH Common Fund Data Resources
PHAROS:  P42575 GTEx:  ENSG00000106144

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide inhibitor (ACE)VDV(3PX)D-CHO	E, F	6	N/A	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
3PX	E,F	L-PEPTIDE LINKING	C8 H15 N O3		PRO

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000786	E, F	Peptide inhibitor (ACE)VDV(3PX)D-CHO	Peptide-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 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.77	α = 90
b = 97.38	β = 90
c = 97.98	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-04-15 
• Released Date: 2011-09-21 
Deposition Author(s): Abendroth, J., Lorimer, D., Stewart, L., Maillard, M., Kiselyov, A.S.

Revision History 

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