Structure of XIAP-BIR1 domain in complex with an NF023 analog

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 

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Structure-Activity Relationship of NF023 Derivatives Binding to XIAP-BIR1.

Sorrentino, L.Cossu, F.Milani, M.Malkoc, B.Huang, W.C.Tsay, S.C.Ru Hwu, J.Mastrangelo, E.

(2019) ChemistryOpen 8: 476-482

  • DOI: https://doi.org/10.1002/open.201900059
  • Primary Citation of Related Structures:  
    6GJW, 6QCI

  • PubMed Abstract: 

    Inhibitors of Apoptosis Proteins (IAPs) are conserved E3-ligases that ubiquitylate substrates to prevent apoptosis and activate the NF-kB survival pathway, often deregulated in cancer. IAPs-mediated regulation of NF-kB signaling is based on the formation of protein complexes by their type-I BIR domains. The XIAP-BIR1 domain dimerizes to bind two TAB1 monomers, leading to downstream NF-kB activation. Thus, impairment of XIAP-BIR1 dimerization could represent a novel strategy to hamper cell survival in cancer. To this aim, we previously reported NF023 as a potential inhibitor of XIAP-BIR1 dimerization. Here we present a thorough analysis of NF023 binding to XIAP-BIR1 through biochemical, biophysical and structural data. The results obtained indicate that XIAP-BIR1 dimerization interface is involved in NF023 binding, and that NF023 overall symmetry and the chemical features of its central moiety are essential for an efficient interaction with the protein. Such strategy provides original hints for the development of novel BIR1-specific compounds as pro-apoptotic agents.

  • Organizational Affiliation

    CNR-IBF Via Celoria 26 I-20133 Milano Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase XIAP
A, B, C, D
111Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P98170 (Homo sapiens)
Explore P98170 
Go to UniProtKB:  P98170
GTEx:  ENSG00000101966 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP98170
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.5α = 90
b = 75.8β = 90
c = 70γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Italian Association for Cancer ResearchItaly17083

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description