1SHJ

Caspase-7 in complex with DICA allosteric inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Discovery of an allosteric site in the caspases

Hardy, J.A., Lam, J., Nguyen, J.T., O'Brien, T., Wells, J.A.

(2004) Proc Natl Acad Sci U S A 101: 12461-12466

  • DOI: 10.1073/pnas.0404781101
  • Primary Citation of Related Structures:  
    1SHL, 1SHJ

  • PubMed Abstract: 

    • Allosteric regulation of proteins by conformational change is a primary means of biological control. Traditionally it has been difficult to identify and characterize novel allosteric sites and ligands that freeze these conformational states. We present a ...

    Allosteric regulation of proteins by conformational change is a primary means of biological control. Traditionally it has been difficult to identify and characterize novel allosteric sites and ligands that freeze these conformational states. We present a site-directed approach using Tethering for trapping inhibitory small molecules at sites away from the active site by reversible disulfide bond formation. We screened a library of 10,000 thiol-containing compounds against accessible cysteines of two members of the caspase family of proteases, caspase-3 and -7. We discovered a previously unreported and conserved allosteric site in a deep cavity at the dimer interface 14 A from the active site. This site contains a natural cysteine that, when disulfide-bonded with either of two specific compounds, inactivates these proteases. The allosteric site is functionally coupled to the active site, such that binding of the compounds at the allosteric site prevents peptide binding at the active site. The x-ray crystal structures of caspase-7 bound by either compound demonstrates that they inhibit caspase-7 by trapping a zymogen-like conformation. This approach may be useful to identify new allosteric sites from natural or engineered cysteines, to study allosteric transitions in proteins, and to nucleate drug discovery efforts.

    Organizational Affiliation: 

    Sunesis Pharmaceuticals, Inc., 341 Oyster Point Boulevard, South San Francisco, CA 94080, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Caspase-7 A, B262Homo sapiensMutation(s): 1 
Gene Names: CASP7, MCH3
EC: 3.4.22 (PDB Primary Data), 3.4.22.60 (UniProt)
Find proteins for P55210 (Homo sapiens)
Explore P55210 
Go to UniProtKB:  P55210
NIH Common Fund Data Resources
PHAROS:  P55210
GTEx:  ENSG00000165806
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NXN
Query on NXN
Download Ideal Coordinates CCD File 
A, B
2-(2,4-DICHLORO-PHENOXY)-N-(2-MERCAPTO-ETHYL)-ACETAMIDE
C10 H11 Cl2 N O2 S
ZKLFUOFLXGWIIY-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.097α = 90
b = 91.097β = 90
c = 184.465γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance