3KJQ

Caspase 8 with covalent inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Kinetic and structural characterization of caspase-3 and caspase-8 inhibition by a novel class of irreversible inhibitors.

Wang, Z.Watt, W.Brooks, N.A.Harris, M.S.Urban, J.Boatman, D.McMillan, M.Kahn, M.Heinrikson, R.L.Finzel, B.C.Wittwer, A.J.Blinn, J.Kamtekar, S.Tomasselli, A.G.

(2010) Biochim Biophys Acta 1804: 1817-1831

  • DOI: 10.1016/j.bbapap.2010.05.007
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Because of their central role in programmed cell death, the caspases are attractive targets for developing new therapeutics against cancer and autoimmunity, myocardial infarction and ischemic damage, and neurodegenerative diseases. We chose to target ...

    Because of their central role in programmed cell death, the caspases are attractive targets for developing new therapeutics against cancer and autoimmunity, myocardial infarction and ischemic damage, and neurodegenerative diseases. We chose to target caspase-3, an executioner caspase, and caspase-8, an initiator caspase, based on the vast amount of information linking their functions to diseases. Through a structure-based drug design approach, a number of novel beta-strand peptidomimetic compounds were synthesized. Kinetic studies of caspase-3 and caspase-8 inhibition were carried out with these urazole ring-containing irreversible peptidomimetics and a known irreversible caspase inhibitor, Z-VAD-fmk. Using a stopped-flow fluorescence assay, we were able to determine individual kinetic parameters of caspase-3 and caspase-8 inhibition by these inhibitors. Z-VAD-fmk and the peptidomimetic inhibitors inhibit caspase-3 and caspase-8 via a three-step kinetic mechanism. Inhibition of both caspase-3 and caspase-8 by Z-VAD-fmk and of caspase-3 by the peptidomimetic inhibitors proceeds via two rapid equilibrium steps followed by a relatively fast inactivation step. However, caspase-8 inhibition by the peptidomimetics goes through a rapid equilibrium step, a slow-binding reversible step, and an extremely slow inactivation step. The crystal structures of inhibitor complexes of caspases-3 and -8 validate the design of the inhibitors by illustrating in detail how they mimic peptide substrates. One of the caspase-8 structures also shows binding at a secondary, allosteric site, providing a possible route to the development of noncovalent small molecule modulators of caspase activity.


    Organizational Affiliation

    Oligonucleotide Therapeutics Unit, Pfizer, Inc., 620 Memorial Drive, Cambridge, MA 02139, USA. zhigang.wang@pfizer.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Caspase-8A164Homo sapiensMutation(s): 0 
Gene Names: CASP8MCH5
EC: 3.4.22.61
Find proteins for Q14790 (Homo sapiens)
Explore Q14790 
Go to UniProtKB:  Q14790
NIH Common Fund Data Resources
PHAROS  Q14790
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Caspase-8B95Homo sapiensMutation(s): 0 
Gene Names: CASP8MCH5
EC: 3.4.22.61
Find proteins for Q14790 (Homo sapiens)
Explore Q14790 
Go to UniProtKB:  Q14790
NIH Common Fund Data Resources
PHAROS  Q14790
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B94
Query on B94

Download CCD File 
A
(3S)-3-({[(5S,8R)-2-(3-carboxypropyl)-8-(2-{[(4-chlorophenyl)acetyl]amino}ethyl)-1,3-dioxo-2,3,5,8-tetrahydro-1H-[1,2,4]triazolo[1,2-a]pyridazin-5-yl]carbonyl}amino)-4-oxopentanoic acid
C26 H30 Cl N5 O9
FCUBCMCZKNHBIS-UFYCRDLUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B94Ki:  1320   nM  Binding MOAD
B94Ki :  1320   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.974α = 90
b = 63.974β = 90
c = 130.847γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance