3H0E | pdb_00003h0e

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

• PDB DOI: https://doi.org/10.2210/pdb3H0E/pdb

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


• Deposited: 2009-04-09 Released: 2009-11-17 
• Deposition Author(s): Xu, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.200 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

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

• PubMed: 19836248 
• DOI: https://doi.org/10.1016/j.bmc.2009.09.036
• Primary Citation of Related Structures:  
  3H0E


• 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.

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Organizational Affiliation: 

Chemical Sciences, Wyeth Research, CN 8000, Princeton, NJ 08543, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.63 kDa 
• Atom Count: 4,179 
• Modelled Residue Count: 475 
• Deposited Residue Count: 510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-3	A, B	255	Homo sapiens	Mutation(s): 0  Gene Names: CASP3, CPP32 EC: 3.4.22.56
UniProt & NIH Common Fund Data Resources
Find proteins for P42574 (Homo sapiens) Explore P42574  Go to UniProtKB:  P42574
PHAROS:  P42574 GTEx:  ENSG00000164305

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H0E	C [auth A], D [auth B]	(10S)-3,3-dimethyl-8-{[(2S)-2-(phenoxymethyl)pyrrolidin-1-yl]sulfonyl}-2,3,4,10-tetrahydropyrimido[1,2-a]indol-10-ol C24 H29 N3 O4 S RPXBZVLBDLIKLZ-JTSKRJEESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.200 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.739	α = 90
b = 69.94	β = 130.08
c = 88.797	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2009-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary