4LGE

Crystal structure of clAP1 BIR3 bound to T3261256


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Design, stereoselective synthesis, and biological evaluation of novel tri-cyclic compounds as inhibitor of apoptosis proteins (IAP) antagonists.

Asano, M.Hashimoto, K.Saito, B.Shiokawa, Z.Sumi, H.Yabuki, M.Yoshimatsu, M.Aoyama, K.Hamada, T.Morishita, N.Dougan, D.R.Mol, C.D.Yoshida, S.Ishikawa, T.

(2013) Bioorg.Med.Chem. 21: 5725-5737

  • DOI: 10.1016/j.bmc.2013.07.020
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We recently reported the discovery of octahydropyrrolo[1,2-a]pyrazine A as a lead compound for an inhibitor of apoptosis proteins (IAP) antagonist. To develop IAP antagonists with favorable PK profiles, we designed novel tri-cyclic compounds, octahyd ...

    We recently reported the discovery of octahydropyrrolo[1,2-a]pyrazine A as a lead compound for an inhibitor of apoptosis proteins (IAP) antagonist. To develop IAP antagonists with favorable PK profiles, we designed novel tri-cyclic compounds, octahydro-1H-cyclopropa[4,5]pyrrolo[1,2-a]pyrazines 1 and 2 based on co-crystal structural analysis of A with cellular IAP-1 (cIAP-1). The additional cyclopropane moiety was used to block the predicted metabolic site of compound A without detriment to the binding affinity for cIAP. Compounds 1 and 2 were stereoselectively synthesized via intermediates 4a and 5b', which were obtained by Simmons-Smith cyclopropanation of ethylester 3a and silyl ether 3b'. Compounds 1 and 2 showed strong growth inhibition in MDA-MB-231 breast cancer cells and improved metabolic stability in comparison to A. Compound 2 exhibited significant in vivo PD effects to increase tumor necrosis factor-alpha mRNA in a dose dependent manner.


    Organizational Affiliation

    Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan. moriteru.asano@takeda.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Baculoviral IAP repeat-containing protein 2
A, B
115Homo sapiensMutation(s): 0 
Gene Names: BIRC2 (API1, MIHB, RNF48)
EC: 2.3.2.27
Find proteins for Q13490 (Homo sapiens)
Go to Gene View: BIRC2
Go to UniProtKB:  Q13490
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
1Y0
Query on 1Y0

Download SDF File 
Download CCD File 
A, B
(4S,6aR,7aS)-5-{(2S)-2-cyclohexyl-2-[(N-methyl-L-alanyl)amino]acetyl}-N-[(4R)-3,4-dihydro-2H-chromen-4-yl]octahydro-1H-cyclopropa[4,5]pyrrolo[1,2-a]pyrazine-4-carboxamide
C30 H43 N5 O4
OGTGKCOHYGILPQ-BBAYRLSSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1Y0IC50: 2.1 nM BINDINGMOAD
1Y0IC50: 3.5 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 30.520α = 90.00
b = 72.805β = 90.00
c = 116.914γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-06-27 
  • Released Date: 2013-08-28 
  • Deposition Author(s): Dougan, D.R.

Revision History 

  • Version 1.0: 2013-08-28
    Type: Initial release