3F7G

Structure of the BIR domain from ML-IAP bound to a peptidomimetic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.167 

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Baculoviral IAP repeat-containing protein 7
A, B, C, D, E
140Homo sapiensMutation(s): 0 
Gene Names: BIRC7 (KIAP, LIVIN, MLIAP, RNF50)
EC: 2.3.2.27
Find proteins for Q96CA5 (Homo sapiens)
Go to Gene View: BIRC7
Go to UniProtKB:  Q96CA5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
389
Query on 389

Download SDF File 
Download CCD File 
E
L-alanyl-L-valyl-N-(2,2-diphenylethyl)-L-prolinamide
C27 H36 N4 O3
ZJCCVSICICQPSQ-IGKWTDBASA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
P33
Query on P33

Download SDF File 
Download CCD File 
D
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
HEPTAETHYLENE GLYCOL, PEG330
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
389Ki: 43 nM (92) BINDINGDB
389Ki: 43 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.167 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 84.016α = 90.00
b = 84.016β = 90.00
c = 94.476γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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