Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 60.73 kDa 
• Atom Count: 3371 
• Modelled Residue Count: 417 
• Deposited Residue Count: 524 
• Unique protein chains: 1

1SHJ

Caspase-7 in complex with DICA allosteric inhibitor

• DOI: 10.2210/pdb1SHJ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-02-25 Released: 2004-08-17 
• Deposition Author(s): Hardy, J.A., Lam, J., Nguyen, J.T., O'Brien, T., Wells, J.A.

---

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 

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

• PubMed: 15314233 
• 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 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-7	A, B	262	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NXN	A, B	2-(2,4-DICHLORO-PHENOXY)-N-(2-MERCAPTO-ETHYL)-ACETAMIDE C10 H11 Cl2 N O2 S ZKLFUOFLXGWIIY-UHFFFAOYSA-N
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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 = 91.097	α = 90
b = 91.097	β = 90
c = 184.465	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-02-25 
• Released Date: 2004-08-17 
Deposition Author(s): Hardy, J.A., Lam, J., Nguyen, J.T., O'Brien, T., Wells, J.A.

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