3GTA

Structure of an ML-IAP/XIAP chimera bound to a peptidomimetic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Antagonists of inhibitor of apoptosis proteins based on thiazole amide isosteres.

Cohen, F.Koehler, M.F.Bergeron, P.Elliott, L.O.Flygare, J.A.Franklin, M.C.Gazzard, L.Keteltas, S.F.Lau, K.Ly, C.Q.Tsui, V.Fairbrother, W.J.

(2010) Bioorg Med Chem Lett 20: 2229-2233

  • DOI: 10.1016/j.bmcl.2010.02.021
  • Primary Citation of Related Structures:  
    3GT9, 3GTA

  • PubMed Abstract: 
  • A series of IAP antagonists based on thiazole or benzothiazole amide isosteres was designed and synthesized. These compounds were tested for binding to the XIAP-BIR3 and ML-IAP BIR using a fluorescence polarization assay. The most potent of these com ...

    A series of IAP antagonists based on thiazole or benzothiazole amide isosteres was designed and synthesized. These compounds were tested for binding to the XIAP-BIR3 and ML-IAP BIR using a fluorescence polarization assay. The most potent of these compounds, 19a and 33b, were found to have K(i)'s of 20-30 nM against ML-IAP and 50-60 nM against XIAP-BIR3.


    Related Citations: 
    • Orally bioavailable antagonists of inhibitor of apoptosis proteins based on an azabicyclooctane scaffold
      Cohen, F., Alicke, B., Elliott, L.O., Flygare, J.A., Goncharov, T., Keteltas, S.F., Franklin, M.C., Frankovitz, S., Stephan, J.P., Tsui, V., Vucic, D., Wong, H., Fairbrother, W.J.
      (2009) J Med Chem 52: 1723
    • Design, synthesis, and biological activity of a potent SMAC mimetic that sensitizes concer cells to apoptosis by antagonizing IAPs.
      Zobel, K., Wang, L., Varfolomeev, E., Franklin, M.C., Elliott, L.O., Wallweber, H.J., Okawa, D.C., Flygare, J.A., Vucic, D., Fairbrother, W.J., Deshayes, K.
      (2006) ACS Chem Biol 1: 525
    • Engineering ML-IAP to produce an extrordinarily potent caspase-9 inhibitor: implications for SMAC-dependent anti-apoptotic activity of ML-IAP
      Vucic, D., Franklin, M.C., Wallweber, H.J., Das, K., Eckelman, B.P., Shin, H., Elliott, L.O., Deshayes, K., Salvesen, G.S., Fairbrother, W.J.
      (2005) Biochem J 385: 11
    • Structure and function analysis of peptide antagonists of melanoma inhibitor of apoptosis (ML-IAP).
      Franklin, M.C., Kadkhodayan, S., Ackerly, H., Alexandru, D., Distefano, M.D., Elliott, L.O., Flygare, J.A., Vucic, D., Deshayes, K., Fairbrother, W.J.
      (2003) Biochemistry 42: 8223

    Organizational Affiliation

    Department of Discovery Chemistry, Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA. fcohen@gene.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Baculoviral IAP repeat-containing 7A, B133Homo sapiensMutation(s): 11 
Gene Names: BIRC7KIAPLIVINMLIAPRNF50UNQ5800/PRO19607/PRO21344
EC: 2.3.2.27
Find proteins for Q96CA5 (Homo sapiens)
Explore Q96CA5 
Go to UniProtKB:  Q96CA5
NIH Common Fund Data Resources
PHAROS  Q96CA5
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
851
Query on 851

Download CCD File 
A, B
N-{(1S)-1-cyclohexyl-2-oxo-2-[(2S)-2-(4-phenyl-1,3-benzothiazol-2-yl)pyrrolidin-1-yl]ethyl}-N~2~-methyl-L-alaninamide
C29 H36 N4 O2 S
ZMBDQSBUBMMIRB-QXWFJRNPSA-N
 Ligand Interaction
BTB
Query on BTB

Download CCD File 
B
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download CCD File 
B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
LI
Query on LI

Download CCD File 
B
LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
851Ki:  53000   nM  BindingDB
851Ki :  53000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.48α = 90
b = 87.48β = 90
c = 74.027γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description