3G76

Crystal structure of XIAP-BIR3 in complex with a bivalent compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for bivalent smac-mimetics recognition in the IAP protein family

Cossu, F.Milani, M.Mastrangelo, E.Vachette, P.Servida, F.Lecis, D.Canevari, G.Delia, D.Drago, C.Rizzo, V.Manzoni, L.Seneci, P.Scolastico, C.Bolognesi, M.

(2009) J Mol Biol 392: 630-644

  • DOI: 10.1016/j.jmb.2009.04.033
  • Primary Citation of Related Structures:  
    3G76

  • PubMed Abstract: 
  • XIAP is an apoptotic regulator protein that binds to the effector caspases -3 and -7 through its BIR2 domain, and to initiator caspase-9 through its BIR3 domain. Molecular docking studies suggested that Smac-DIABLO may antagonize XIAP by concurrently targeting both BIR2 and BIR3 domains; on this basis bivalent Smac-mimetic compounds have been proposed and characterized ...

    XIAP is an apoptotic regulator protein that binds to the effector caspases -3 and -7 through its BIR2 domain, and to initiator caspase-9 through its BIR3 domain. Molecular docking studies suggested that Smac-DIABLO may antagonize XIAP by concurrently targeting both BIR2 and BIR3 domains; on this basis bivalent Smac-mimetic compounds have been proposed and characterized. Here, we report the X-ray crystal structure of XIAP-BIR3 domain in complex with a two-headed compound (compound 3) with improved efficacy relative to its monomeric form. A small-angle X-ray scattering study of XIAP-BIR2BIR3, together with fluorescence polarization binding assays and compound 3 cytotoxicity tests on HL60 leukemia cell line are also reported. The crystal structure analysis reveals a network of interactions supporting XIAP-BIR3/compound 3 recognition; moreover, analytical gel-filtration chromatography shows that compound 3 forms a 1:1 stoichiometric complex with a XIAP protein construct containing both BIR2 and BIR3 domains. On the basis of the crystal structure and small-angle X-ray scattering, a model of the same BIR2-BIR3 construct bound to compound 3 is proposed, shedding light on the ability of compound 3 to relieve XIAP inhibitory effects on caspase-9 as well as caspases -3 and -7. A molecular modeling/docking analysis of compound 3 bound to cIAP1-BIR3 domain is presented, considering that Smac-mimetics have been shown to kill tumor cells by inducing cIAP1 and cIAP2 ubiquitination and degradation. Taken together, the results reported here provide a rationale for further development of compound 3 as a lead in the design of dimeric Smac mimetics for cancer treatment.


    Organizational Affiliation

    Department of Biomolecular Sciences and Biotechnology, University of Milano, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Baculoviral IAP repeat-containing protein 4A, B, C, D, E, F, G, H122Homo sapiensMutation(s): 0 
Gene Names: XIAPAPI3BIRC4IAP3
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for P98170 (Homo sapiens)
Explore P98170 
Go to UniProtKB:  P98170
NIH Common Fund Data Resources
PHAROS:  P98170
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CZ3
Query on CZ3

Download Ideal Coordinates CCD File 
J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth F], V [auth G], X [auth H]1,1'-{hexa-2,4-diyne-1,6-diylbis[oxy{(2S,3R)-2-[(N-methyl-L-alanyl)amino]-1-oxobutane-3,1-diyl}(2S)pyrrolidine-1,2-diylmethanediyl]}bis[5-(phenylsulfanyl)-1H-tetrazole]
C46 H60 N14 O6 S2
CDUYVSXKBIKUNH-RAUIGOKHSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], U [auth G], W [auth H]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CZ3IC50 :  230.8000030517578   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.235 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.077α = 90
b = 119.077β = 90
c = 105.59γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance