3,4-Dihydropyrimido(1,2-a)indol-10(2H)-ones as Potent Non-Peptidic Inhibitors of Caspase-3

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 

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3,4-Dihydropyrimido(1,2-a)indol-10(2H)-ones as potent non-peptidic inhibitors of caspase-3

Havran, L.M.Chong, D.C.Childers, W.E.Dollings, P.J.Dietrich, A.Harrison, B.L.Marathias, V.Tawa, G.Aulabaugh, A.Cowling, R.Kapoor, B.Xu, W.Mosyak, L.Moy, F.Hum, W.T.Wood, A.Robichaud, A.J.

(2009) Bioorg Med Chem 17: 7755-7768

  • DOI: https://doi.org/10.1016/j.bmc.2009.09.036
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Cysteine-dependant aspartyl protease (caspase) activation has been implicated as a part of the signal transduction pathway leading to apoptosis. It has been postulated that caspase-3 inhibition could attenuate cell damage after an ischemic event and thereby providing for a novel neuroprotective treatment for stroke. As part of a program to develop a small molecule inhibitor of caspase-3, a novel series of 3,4-dihydropyrimido(1,2-a)indol-10(2H)-ones (pyrimidoindolones) was identified. The synthesis, biological evaluation and structure-activity relationships of the pyrimidoindolones are described.

  • Organizational Affiliation

    Chemical Sciences, Wyeth Research, CN 8000, Princeton, NJ 08543, USA. havranl@wyeth.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
255Homo sapiensMutation(s): 0 
Gene Names: CASP3CPP32
UniProt & NIH Common Fund Data Resources
Find proteins for P42574 (Homo sapiens)
Explore P42574 
Go to UniProtKB:  P42574
PHAROS:  P42574
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42574
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on H0E

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C24 H29 N3 O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
H0E PDBBind:  3H0E IC50: 7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.739α = 90
b = 69.94β = 130.08
c = 88.797γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2009-11-17 
  • Deposition Author(s): Xu, W.

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance