1GFW

THE 2.8 ANGSTROM CRYSTAL STRUCTURE OF CASPASE-3 (APOPAIN OR CPP32)IN COMPLEX WITH AN ISATIN SULFONAMIDE INHIBITOR.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

Potent and selective nonpeptide inhibitors of caspases 3 and 7 inhibit apoptosis and maintain cell functionality.

Lee, D., Long, S.A., Adams, J.L., Chan, G., Vaidya, K.S., Francis, T.A., Kikly, K., Winkler, J.D., Sung, C.M., Debouck, C., Richardson, S., Levy, M.A., DeWolf Jr., W.E., Keller, P.M., Tomaszek, T., Head, M.S., Ryan, M.D., Haltiwanger, R.C., Liang, P.H., Janson, C.A., McDevitt, P.J., Johanson, K., Concha, N.O., Chan, W., Abdel-Meguid, S.S., Badger, A.M., Lark, M.W., Nadeau, D.P., Suva, L.J., Gowen, M., Nuttall, M.E.

(2000) J Biol Chem 275: 16007-16014

  • DOI: 10.1074/jbc.275.21.16007
  • Primary Citation of Related Structures:  
    1GFW

  • PubMed Abstract: 

    • Caspases have been strongly implicated to play an essential role in apoptosis. A critical question regarding the role(s) of these proteases is whether selective inhibition of an effector caspase(s) will prevent cell death. We have identified potent and s ...

    Caspases have been strongly implicated to play an essential role in apoptosis. A critical question regarding the role(s) of these proteases is whether selective inhibition of an effector caspase(s) will prevent cell death. We have identified potent and selective non-peptide inhibitors of the effector caspases 3 and 7. The inhibition of apoptosis and maintenance of cell functionality with a caspase 3/7-selective inhibitor is demonstrated for the first time, and suggests that targeting these two caspases alone is sufficient for blocking apoptosis. Furthermore, an x-ray co-crystal structure of the complex between recombinant human caspase 3 and an isatin sulfonamide inhibitor has been solved to 2.8-A resolution. In contrast to previously reported peptide-based caspase inhibitors, the isatin sulfonamides derive their selectivity for caspases 3 and 7 by interacting primarily with the S(2) subsite, and do not bind in the caspase primary aspartic acid binding pocket (S(1)). These inhibitors blocked apoptosis in murine bone marrow neutrophils and human chondrocytes. Furthermore, in camptothecin-induced chondrocyte apoptosis, cell functionality as measured by type II collagen promoter activity is maintained, an activity considered essential for cartilage homeostasis. These data suggest that inhibiting chondrocyte cell death with a caspase 3/7-selective inhibitor may provide a novel therapeutic approach for the prevention and treatment of osteoarthritis, or other disease states characterized by excessive apoptosis.

    Related Citations: 
    • CPP32, a novel human apoptotic protein with homology to Caenorhabditis elegans cell death protein ced-3 and mammalian interleukin-1-b-converting enzyme
      Fernandes-Alnemri, T., Litwack, G., Alnemri, E.S.
      (1994) J Biol Chem 269: 30761
    Organizational Affiliation: 

    Department of Medicinal Chemistry, SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CASPASE-3 (APOPAIN, P20) A147Homo sapiensMutation(s): 0 
Gene Names: CASP3, CPP32
EC: 3.4.22.56
Find proteins for P42574 (Homo sapiens)
Explore P42574 
Go to UniProtKB:  P42574
NIH Common Fund Data Resources
PHAROS:  P42574
GTEx:  ENSG00000164305
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CASPASE-3 (APOPAIN, P10) B97Homo sapiensMutation(s): 0 
Gene Names: CASP3, CPP32
EC: 3.4.22.56
Find proteins for P42574 (Homo sapiens)
Explore P42574 
Go to UniProtKB:  P42574
NIH Common Fund Data Resources
PHAROS:  P42574
GTEx:  ENSG00000164305
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MSI
Query on MSI
Download Ideal Coordinates CCD File 
A
1-METHYL-5-(2-PHENOXYMETHYL-PYRROLIDINE-1-SULFONYL)-1H-INDOLE-2,3-DIONE
C20 H20 N2 O5 S
PFAYCUAUBOGVDX-AWEZNQCLSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MSIΔG:  42.63999938964844   kJ/mol  BindingDB
MSI-TΔS:  3.0999999046325684   kJ/mol  BindingDB
MSIKi:  11   nM  BindingDB
MSIEC50:  7670   nM  BindingDB
MSIIC50:  30   nM  BindingDB
MSIΔG:  43.04999923706055   kJ/mol  BindingDB
MSIΔG:  42.220001220703125   kJ/mol  BindingDB
MSIIC50:  114   nM  BindingDB
MSI-TΔS:  2.680000066757202   kJ/mol  BindingDB
MSIKi:  56.099998474121094   nM  BindingDB
MSIIC50:  120.2300033569336   nM  BindingDB
MSIIC50:  119.19999694824219   nM  BindingDB
MSIIC50:  2.4000000953674316   nM  BindingDB
MSI-TΔS:  1.850000023841858   kJ/mol  BindingDB
MSIKi:  15   nM  BindingDB
MSIKi :  15   nM  PDBBind
MSIIC50:  10000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.200 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.2α = 90
b = 83.3β = 90
c = 96γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement
MAR345data collection

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-06-23
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Advisory, Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.5: 2019-08-14
    Changes: Data collection