6EXW

Crystal structure of cIAP1-BIR3 in complex with a covalently bound SM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-based design and molecular profiling of Smac-mimetics selective for cellular IAPs.

Corti, A.Milani, M.Lecis, D.Seneci, P.de Rosa, M.Mastrangelo, E.Cossu, F.

(2018) FEBS J 285: 3286-3298

  • DOI: 10.1111/febs.14616
  • Primary Citation of Related Structures:  
    6EY2, 6EXW

  • PubMed Abstract: 
  • Inhibitor of Apoptosis Proteins (IAPs) is highly conserved negative regulators of apoptosis overexpressed in many cancer cells. Based on their endogenous antagonist, Smac/DIABLO, mimic compounds (Smac-mimetics, SMs) have been developed to inhibit IAP ...

    Inhibitor of Apoptosis Proteins (IAPs) is highly conserved negative regulators of apoptosis overexpressed in many cancer cells. Based on their endogenous antagonist, Smac/DIABLO, mimic compounds (Smac-mimetics, SMs) have been developed to inhibit IAPs prosurvival activity, showing promising effects in advanced phases of clinical trials. Since different IAP homologs play distinctive roles in cancer cell survival and immunomodulation, SM-induced apoptosis proceeds through diverse mechanisms. After binding to their BIR3 domain, SMs have been shown to rapidly induce auto-ubiquitylation and degradation of cellular IAPs (cIAPs), thus leading to cell death mainly by activation of the noncanonical NF-κB pathway. For this reason, we started the BIR3-driven design of compounds selective for cIAP1 and with reduced affinity for X-linked IAP (XIAP), in order to focus SMs antitumor activity on cIAPs degradation. In this work, we describe the crystal structures of the BIR3 domains of cIAP1 and XIAP, each in complex with a cIAP1-selective SM (SM130 and SM114, respectively). The two SMs displayed 23- and 32-fold higher affinity for cIAP1-BIR3 over XIAP-BIR3 in molecular displacement experiments based on fluorescence polarization. In vitro cell-based assays confirmed that both selective SMs triggered apoptosis in cancer cells with different efficiencies by inducing caspases-3, -8, and -9-independent cIAP1 degradation. The design of cIAPs-selective compounds represents an innovative approach in the field of anticancer drugs development, being useful to elucidate different prosurvival mechanisms and to reduce the adverse effects of pan-IAPs compounds in cancer therapy.


    Organizational Affiliation

    Dipartimento di Bioscienze, Università di Milano, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Baculoviral IAP repeat-containing protein 2AC122Homo sapiensMutation(s): 0 
Gene Names: BIRC2API1MIHBRNF48
EC: 2.3.2.27
Find proteins for Q13490 (Homo sapiens)
Explore Q13490 
Go to UniProtKB:  Q13490
NIH Common Fund Data Resources
PHAROS  Q13490
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C3K
Query on C3K

Download CCD File 
A, C
(3~{S},6~{S},7~{R},9~{a}~{S})-6-[[(2~{S})-2-(methylamino)propanoyl]amino]-5-oxidanylidene-~{N}-(phenylmethyl)-7-[(propanoylamino)methyl]-3,6,7,8,9,9~{a}-hexahydropyrrolo[1,2-a]azepine-3-carboxamide
C25 H35 N5 O4
JUEBKGOOCOQQTH-ZFVOUSBOSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.799α = 90
b = 53.799β = 90
c = 176.627γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
AIRCItalyAIRC MFAG 17083

Revision History 

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-09-19
    Changes: Data collection, Database references