Crystal structure of CASPASE-7 in Complex with allosteric inhibitor

Experimental Data Snapshot

  • Resolution: 3.79 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.242 

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A class of allosteric caspase inhibitors identified by high-throughput screening.

Feldman, T.Kabaleeswaran, V.Jang, S.B.Antczak, C.Djaballah, H.Wu, H.Jiang, X.

(2012) Mol Cell 47: 585-595

  • DOI: https://doi.org/10.1016/j.molcel.2012.06.007
  • Primary Citation of Related Structures:  
    4FDL, 4FEA

  • PubMed Abstract: 

    Caspase inhibition is a promising approach for treating multiple diseases. Using a reconstituted assay and high-throughput screening, we identified a group of nonpeptide caspase inhibitors. These inhibitors share common chemical scaffolds, suggesting the same mechanism of action. They can inhibit apoptosis in various cell types induced by multiple stimuli; they can also inhibit caspase-1-mediated interleukin generation in macrophages, indicating potential anti-inflammatory application. While these compounds inhibit all the tested caspases, kinetic analysis indicates they do not compete for the catalytic sites of the enzymes. The cocrystal structure of one of these compounds with caspase-7 reveals that it binds to the dimerization interface of the caspase, another common structural element shared by all active caspases. Consistently, biochemical analysis demonstrates that the compound abates caspase-8 dimerization. Based on these kinetic, biochemical, and structural analyses, we suggest that these compounds are allosteric caspase inhibitors that function through binding to the dimerization interface of caspases.

  • Organizational Affiliation

    Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
247Homo sapiensMutation(s): 0 
Gene Names: CASP7MCH3
UniProt & NIH Common Fund Data Resources
Find proteins for P55210 (Homo sapiens)
Explore P55210 
Go to UniProtKB:  P55210
PHAROS:  P55210
GTEx:  ENSG00000165806 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55210
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0TE

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
chloro{methyl hydrogenato(3-)-kappa~2~N,S [pyridin-2-yl(pyridin-2(1H)-ylidene-kappaN)methyl]carbonodithiohydrazonate}copper
C13 H11 Cl Cu N4 S2
Binding Affinity Annotations 
IDSourceBinding Affinity
0TE PDBBind:  4FEA Ki: 340 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.79 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.242 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.72α = 90
b = 88.72β = 90
c = 185.66γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-01
    Type: Initial release
  • Version 1.1: 2012-09-12
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description