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 selective non-peptide inhibitors of the effector caspases 3 and 7 ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CASPASE-3 (APOPAIN, P20)A147Homo sapiensMutation(s): 0 
Gene Names: CASP3CPP32
EC: 3.4.22.56
UniProt & NIH Common Fund Data Resources
Find proteins for P42574 (Homo sapiens)
Explore P42574 
Go to UniProtKB:  P42574
PHAROS:  P42574
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42574
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CASPASE-3 (APOPAIN, P10)B97Homo sapiensMutation(s): 0 
Gene Names: CASP3CPP32
EC: 3.4.22.56
UniProt & NIH Common Fund Data Resources
Find proteins for P42574 (Homo sapiens)
Explore P42574 
Go to UniProtKB:  P42574
PHAROS:  P42574
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42574
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 
C [auth A]1-METHYL-5-(2-PHENOXYMETHYL-PYRROLIDINE-1-SULFONYL)-1H-INDOLE-2,3-DIONE
C20 H20 N2 O5 S
PFAYCUAUBOGVDX-AWEZNQCLSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
MSI BindingDB:  1GFW Ki: min: 11, max: 56.1 (nM) from 3 assay(s)
IC50: min: 2.4, max: 1.00e+4 (nM) from 6 assay(s)
EC50: 7670 (nM) from 1 assay(s)
-TΔS: min: 1.85, max: 3.1 (kJ/mol) from 3 assay(s)
ΔG: min: -4.31e+1, max: -4.22e+1 (kJ/mol) from 3 assay(s)
PDBBind:  1GFW Ki: 15 (nM) from 1 assay(s)
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




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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