2I3H

Structure of an ML-IAP/XIAP chimera bound to a 4-mer peptide (AVPW)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 525-533

  • DOI: 10.1021/cb600276q
  • Primary Citation of Related Structures:  
  • Also Cited By: 3GTA, 3GT9, 3F7I, 3F7H, 3F7G

  • PubMed Abstract: 
  • Designed second mitochondrial activator of caspases (Smac) mimetics based on an accessible [7,5]-bicyclic scaffold bind to and antagonize protein interactions involving the inhibitor of apoptosis (IAP) proteins, X-chromosome-linked IAP (XIAP), melano ...

    Designed second mitochondrial activator of caspases (Smac) mimetics based on an accessible [7,5]-bicyclic scaffold bind to and antagonize protein interactions involving the inhibitor of apoptosis (IAP) proteins, X-chromosome-linked IAP (XIAP), melanoma IAP (ML-IAP), and c-IAPs 1 and 2 (cIAP1 and cIAP2). The design rationale is based on a combination of phage-panning data, peptide binding studies, and a survey of potential isosteres. The synthesis of two scaffolds is described. These compounds bind the XIAP-baculoviral IAP repeat 3 (BIR3), cIAP1-BIR3, cIAP2-BIR3, and ML-IAP-BIR domains with submicromolar affinities. The most potent Smac mimetic binds the cIAP1-BIR3 and ML-IAP-BIR domains with a K i of 50 nM. The X-ray crystal structure of this compound bound to an ML-IAP/XIAP chimeric BIR domain protein is compared with that of a complex with a phage-derived tetrapeptide, AVPW. The structures show that these compounds bind to the Smac-binding site on ML-IAP with identical hydrogen-bonding patterns and similar hydrophobic interactions. Consistent with the structural data, coimmunoprecipitation experiments demonstrate that the compounds can effectively block Smac interactions with ML-IAP. The compounds are further demonstrated to activate caspase-3 and -7, to reduce cell viability in assays using MDA-MB-231 breast cancer cells and A2058 melanoma cells, and to enhance doxorubicin-induced apoptosis in MDA-MB-231 cells.


    Related Citations: 
    • 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
    • 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


    Organizational Affiliation

    Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Baculoviral IAP repeat-containing protein 7
A, B
133Homo 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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
AVPW peptide
C, D
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 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
LI
Query on LI

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Download CCD File 
B
LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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

Download SDF File 
Download CCD File 
B
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
BIS-TRIS BUFFER
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.161 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 87.541α = 90.00
b = 87.541β = 90.00
c = 73.876γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance