3F7I

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 1723-1730

  • DOI: 10.1021/jm801450c
  • Primary Citation of Related Structures:  
    3F7G, 3F7H, 3F7I

  • PubMed Abstract: 
  • A series of IAP antagonists based on an azabicyclooctane scaffold was designed and synthesized. The most potent of these compounds, 14b, binds to the XIAP BIR3 domain, the BIR domain of ML-IAP, and the BIR3 domain of c-IAP1 with K(i) values of 140, 3 ...

    A series of IAP antagonists based on an azabicyclooctane scaffold was designed and synthesized. The most potent of these compounds, 14b, binds to the XIAP BIR3 domain, the BIR domain of ML-IAP, and the BIR3 domain of c-IAP1 with K(i) values of 140, 38, and 33 nM, respectively. These compounds promote degradation of c-IAP1, activate caspases, and lead to decreased viability of breast cancer cells without affecting normal mammary epithelial cells. Finally, compound 14b inhibits tumor growth when dosed orally in a breast cancer xenograft model.


    Related Citations: 
    • Design, synthesis, and biological activity of a potent Smac mimetic that sensitizes cancer 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 extraordinarily 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

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Baculoviral IAP repeat-containing protein 7AB133Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G13
Query on G13

Download CCD File 
A, B
N-[(3aR,6S,6aS)-1-(N-methyl-L-alanyl-3-methyl-L-valyl)octahydrocyclopenta[b]pyrrol-6-yl]naphthalene-1-carboxamide
C28 H38 N4 O3
FTXKVJPIFDKIID-YBAXTEPTSA-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 %)
G13Ki:  46   nM  BindingDB
G13Ki :  46   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.163α = 90
b = 87.163β = 90
c = 73.685γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description