1NME

Structure of Casp-3 with tethered salicylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • 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 ...

    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. erlanson@sunesis.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Caspase-3 A146Homo sapiensMutation(s): 0 
Gene Names: CASP3CPP32
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Caspase-3 B92Homo sapiensMutation(s): 0 
Gene Names: CASP3CPP32
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
159
Query on 159

Download Ideal Coordinates CCD File 
B
2-HYDROXY-5-(2-MERCAPTO-ETHYLSULFAMOYL)-BENZOIC ACID
C9 H11 N O5 S2
UCQUNSCHVXCSCJ-UHFFFAOYSA-N
 Ligand Interaction
158
Query on 158

Download Ideal Coordinates CCD File 
A
3-(2-MERCAPTO-ACETYLAMINO)-4-OXO-PENTANOIC ACID
C7 H11 N O4 S
BSLDCFOJAJXQLY-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.176 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.488α = 90
b = 83.598β = 90
c = 95.6γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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