Crystal structure of procaspase-8 in complex with covalent small molecule inhibitor 63-R

Experimental Data Snapshot

  • Resolution: 2.88 Å
  • R-Value Free: 0.366 
  • R-Value Work: 0.286 
  • R-Value Observed: 0.289 

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Integrative X-ray Structure and Molecular Modeling for the Rationalization of Procaspase-8 Inhibitor Potency and Selectivity.

Xu, J.H.Eberhardt, J.Hill-Payne, B.Gonzalez-Paez, G.E.Castellon, J.O.Cravatt, B.F.Forli, S.Wolan, D.W.Backus, K.M.

(2020) ACS Chem Biol 15: 575-586

  • DOI: https://doi.org/10.1021/acschembio.0c00019
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Caspases are a critical class of proteases involved in regulating programmed cell death and other biological processes. Selective inhibitors of individual caspases, however, are lacking, due in large part to the high structural similarity found in the active sites of these enzymes. We recently discovered a small-molecule inhibitor, 63- R , that covalently binds the zymogen, or inactive precursor (pro-form), of caspase-8, but not other caspases, pointing to an untapped potential of procaspases as targets for chemical probes. Realizing this goal would benefit from a structural understanding of how small molecules bind to and inhibit caspase zymogens. There have, however, been very few reported procaspase structures. Here, we employ X-ray crystallography to elucidate a procaspase-8 crystal structure in complex with 63- R , which reveals large conformational changes in active-site loops that accommodate the intramolecular cleavage events required for protease activation. Combining these structural insights with molecular modeling and mutagenesis-based biochemical assays, we elucidate key interactions required for 63- R inhibition of procaspase-8. Our findings inform the mechanism of caspase activation and its disruption by small molecules and, more generally, have implications for the development of small molecule inhibitors and/or activators that target alternative (e.g., inactive precursor) protein states to ultimately expand the druggable proteome.

  • Organizational Affiliation

    Departments of Biological Chemistry and Chemistry and Biochemistry, David Geffen School of Medicine , University of California, Los Angeles , 405 Hilgard Avenue , Los Angeles , California 90095 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
274Homo sapiensMutation(s): 4 
Gene Names: CASP8MCH5
UniProt & NIH Common Fund Data Resources
Find proteins for Q14790 (Homo sapiens)
Explore Q14790 
Go to UniProtKB:  Q14790
PHAROS:  Q14790
GTEx:  ENSG00000064012 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14790
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 63R

Download Ideal Coordinates CCD File 
G [auth B]N-{(3R)-1-[4-(morpholin-4-yl)benzene-1-carbonyl]piperidin-3-yl}-N-phenylacetamide
C24 H29 N3 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.88 Å
  • R-Value Free: 0.366 
  • R-Value Work: 0.286 
  • R-Value Observed: 0.289 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.311α = 90
b = 101.311β = 90
c = 175.547γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM118382
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM069832
Department of Energy (DOE, United States)United StatesDE-FC02-02ER63421

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2020-03-04
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description