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)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.97 kDa 
• Atom Count: 4531 
• Residue Count: 480 
• Unique protein chains: 1

1NMS

Caspase-3 tethered to irreversible inhibitor

• DOI: 10.2210/pdb1NMS/pdb

• Classification: APOPTOSIS, HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-01-10 Released: 2003-03-11 
• Deposition Author(s): Erlanson, D.A., Lam, J., Wiesmann, C., Luong, T.N., Simmons, R.L., DeLano, W.L., Choong, I.C., Flanagan, W.M., Lee, D., O'Brian, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.183 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 

Literature

In situ assembly of enzyme inhibitors using extended tethering.

Erlanson, D.A., Lam, J.W., Wiesmann, C., Luong, T.N., Simmons, R.L., DeLano, W.L., Choong, I.C., Burdett, M.T., Flanagan, W.M., Lee, D., Gordon, E.M., O'Brien, T.

(2003) Nat Biotechnol 21: 308-314

• PubMed: 12563278 
• DOI: 10.1038/nbt786
• Primary Citation of Related Structures:  
  1NME, 1NMS, 1NMQ


• PubMed Abstract: 
  

Cysteine aspartyl protease-3 (caspase-3) is a mediator of apoptosis and a therapeutic target for a wide range of diseases. Using a dynamic combinatorial technology, 'extended tethering', we identified unique nonpeptidic inhibitors for this enzyme. Extended tethering allowed the identification of ligands that bind to discrete regions of caspase-3 and also helped direct the assembly of these ligands into small-molecule inhibitors. We first designed a small-molecule 'extender' that irreversibly alkylates the cysteine residue of caspase-3 and also contains a thiol group. The modified protein was then screened against a library of disulfide-containing small-molecule fragments. Mass-spectrometry was used to identify ligands that bind noncovalently to the protein and that also form a disulfide linkage with the extender. Linking the selected fragments with binding elements from the extenders generates reversible, tight-binding molecules that are druglike and distinct from known inhibitors. One molecule derived from this approach inhibited apoptosis in cells.

---

Related Citations: 

• Identification of Potent and Selective Small-Molecule Inhibitors of Caspase-3 through the Use of Extended Tethering and Structure-Based Drug Design
  Choong, I.C., Lew, W., Lee, D., Pham, P., Burdett, M.T., Lam, J.W., Wiesmann, C., Luong, T.N., Fahr, B., O'Brian, T.
  (2002) J Med Chem 45: 5005

---

Organizational Affiliation: 

Sunesis Pharmaceuticals, Inc., 341 Oyster Point Boulevard, South San Francisco, CA 94080, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-3	A, B	249	Homo sapiens	Mutation(s): 0  Gene Names: CASP3, CPP32 EC: 3.4.22 (PDB Primary Data), 3.4.22.56 (UniProt)
Find proteins for P42574 (Homo sapiens) Explore P42574  Go to UniProtKB:  P42574
NIH Common Fund Data Resources
PHAROS:  P42574 GTEx:  ENSG00000164305

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
161	A, B	5-[4-(1-CARBOXYMETHYL-2-OXO-PROPYLCARBAMOYL)-BENZYLSULFAMOYL]-2-HYDROXY-BENZOIC ACID C20 H20 N2 O9 S LBAHOXPDTNUYCX-INIZCTEOSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
161	Ki :  200   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.183 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.45	α = 90
b = 70.952	β = 136.42
c = 95.86	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-01-10 
• Released Date: 2003-03-11 
Deposition Author(s): Erlanson, D.A., Lam, J., Wiesmann, C., Luong, T.N., Simmons, R.L., DeLano, W.L., Choong, I.C., Flanagan, W.M., Lee, D., O'Brian, T.

Revision History 

• Version 1.0: 2003-03-11
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance