1SHL

CASPASE-7 IN COMPLEX WITH FICA ALLOSTERIC INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.3 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.USA 101: 12461-12466

  • DOI: 10.1073/pnas.0404781101
  • Primary Citation of Related Structures:  

  • 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 prese ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Caspase-7
A, B
245Homo sapiensMutation(s): 1 
Gene Names: CASP7 (MCH3)
EC: 3.4.22.60
Find proteins for P55210 (Homo sapiens)
Go to Gene View: CASP7
Go to UniProtKB:  P55210
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FXN
Query on FXN

Download SDF File 
Download CCD File 
A, B
5-FLUORO-1H-INDOLE-2-CARBOXYLIC ACID-(2-MERCAPTO-ETHYL)-AMIDE
FICA
C11 H11 F N2 O S
JFUIHGAGFMFNRD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.221 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.220α = 90.00
b = 90.220β = 90.00
c = 186.621γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-08-23
    Type: Advisory, Refinement description, Source and taxonomy