1RHM

CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-3 WITH A NICOTINIC ACID ALDEHYDE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Reducing the Peptidyl Features of Caspase-3 Inhibitors: A Structural Analysis.

Becker, J.W.Rotonda, J.Soisson, S.M.Aspiotis, R.Bayly, C.Francoeur, S.Gallant, M.Garcia-Calvo, M.Giroux, A.Grimm, E.Han, Y.McKay, D.Nicholson, D.W.Peterson, E.Renaud, J.Roy, S.Thornberry, N.Zamboni, R.

(2004) J.Med.Chem. 47: 2466-2474

  • DOI: 10.1021/jm0305523
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Caspases are cysteine proteases that specifically cleave Asp-Xxx bonds. They are key agents in inflammation and apoptosis and are attractive targets for therapy against inflammation, neurodegeneration, ischemia, and cancer. Many caspase structures ar ...

    Caspases are cysteine proteases that specifically cleave Asp-Xxx bonds. They are key agents in inflammation and apoptosis and are attractive targets for therapy against inflammation, neurodegeneration, ischemia, and cancer. Many caspase structures are known, but most involve either peptide or protein inhibitors, unattractive candidates for drug development. We present seven crystal structures of inhibited caspase-3 that illustrate several approaches to reducing the peptidyl characteristics of the inhibitors while maintaining their potency and selectivity. The inhibitors reduce the peptidyl nature of inhibitors while preserving binding potency by (1). exploiting a hydrophobic binding site C-terminal to the cleavage site, (2). replacing the negatively charged aspartyl residue at P4 with neutral groups, and (3). using a peptidomimetic 5,6,7-tricyclic system or a pyrazinone at P2-P3. In addition, we have found that two nicotinic acid aldehydes induce a significant conformational change in the S2 and S3 subsites of caspase-3, revealing an unexpected binding mode. These results advance the search for caspase-directed drugs by revealing how unacceptable molecular features can be removed without loss of potency.


    Organizational Affiliation

    Departments of Medicinal Chemistry and Metabolic Disorders, Merck Research Laboratory, PO Box 2000, Rahway, New Jersey 07065, USA. joseph_becker@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CASP-3
A, C
147Homo sapiensMutation(s): 0 
Gene Names: CASP3 (CPP32)
EC: 3.4.22.56
Find proteins for P42574 (Homo sapiens)
Go to Gene View: CASP3
Go to UniProtKB:  P42574
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CASP-3
B, D
102Homo sapiensMutation(s): 0 
Gene Names: CASP3 (CPP32)
EC: 3.4.22.56
Find proteins for P42574 (Homo sapiens)
Go to Gene View: CASP3
Go to UniProtKB:  P42574
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA4
Query on NA4

Download SDF File 
Download CCD File 
A, C
4-[5-(2-CARBOXY-1-FORMYL-ETHYLCARBAMOYL)-PYRIDIN-3-YL]-BENZOIC ACID
C17 H14 N2 O6
JNRAPROKLOUIRA-AWEZNQCLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NA4IC50: 1735 nM (100) BINDINGDB
NA4IC50: 1735 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 125.065α = 90.00
b = 70.902β = 129.20
c = 86.567γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-GENdata reduction
CNXrefinement
SAINTdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-11
    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: 2017-10-11
    Type: Refinement description