1RHU

CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-3 WITH A 5,6,7 TRICYCLIC PEPTIDOMIMETIC INHIBITOR

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.166 

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:  
    1RE1, 1RHM, 1RHK, 1RHJ, 1RHU, 1RHR, 1RHQ

  • 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 are known, but most involve either peptide or protein inhibitors, unattractive candidates for drug development ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Caspase-3 A147Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Caspase-3 B102Homo sapiensMutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3CY
Query on 3CY
Download Ideal Coordinates CCD File 
A
(3S)-3-[({(2S)-5-[(N-ACETYL-L-ALPHA-ASPARTYL)AMINO]-4-OXO-1,2,4,5,6,7-HEXAHYDROAZEPINO[3,2,1-HI]INDOL-2-YL}CARBONYL)AMINO]-5-(BENZYLSULFANYL)-4-OXOPENTANOIC ACID
C31 H34 N4 O9 S
PEECWFLPGAWBQR-ZJZGAYNASA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3CYIC50 :  3   nM  PDBBind
3CYIC50:  3   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.166 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.5α = 90
b = 98β = 90
c = 44γ = 90
Software Package:
Software NamePurpose
CNXrefinement
X-GENdata reduction
SAINTdata scaling
X-PLORphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description