3MUP

cIAP1-BIR3 domain in complex with the Smac-mimetic compound Smac037


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Recognition of Smac-mimetic compounds by the BIR domain of cIAP1

Cossu, F.Malvezzi, F.Canevari, G.Mastrangelo, E.Lecis, D.Delia, D.Seneci, P.Scolastico, C.Bolognesi, M.Milani, M.

(2010) Protein Sci 19: 2418-2429

  • DOI: https://doi.org/10.1002/pro.523
  • Primary Citation of Related Structures:  
    3MUP, 3OZ1

  • PubMed Abstract: 

    Inhibitor of apoptosis proteins (IAPs) are negative regulators of apoptosis. As IAPs are overexpressed in many tumors, where they confer chemoresistance, small molecules inactivating IAPs have been proposed as anticancer agents. Accordingly, a number of IAP-binding pro-apoptotic compounds that mimic the sequence corresponding to the N-terminal tetrapeptide of Smac/DIABLO, the natural endogenous IAPs inhibitor, have been developed. Here, we report the crystal structures of the BIR3 domain of cIAP1 in complex with Smac037, a Smac-mimetic known to bind potently to the XIAP-BIR3 domain and to induce degradation of cIAP1, and in complex with the novel Smac-mimetic compound Smac066. Thermal stability and fluorescence polarization assays show the stabilizing effect and the high affinity of both Smac037 and Smac066 for cIAP1- and cIAP2-BIR3 domains.


  • Organizational Affiliation

    Dipartimento di Scienze Biomolecolari e Biotecnologie, Università di Milano, Via Celoria 26, I-20133, Milano, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Baculoviral IAP repeat-containing protein 2
A, B, C, D
122Homo sapiensMutation(s): 0 
Gene Names: API1BIRC2IAP2MIHBRNF48
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q13490 (Homo sapiens)
Explore Q13490 
Go to UniProtKB:  Q13490
PHAROS:  Q13490
GTEx:  ENSG00000110330 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13490
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SMK
Query on SMK

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
(3S,6S,7R,9aS)-6-{[(2S)-2-aminobutanoyl]amino}-7-(2-aminoethyl)-N-(diphenylmethyl)-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide
C29 H39 N5 O3
KQHWCFZCUNTTCW-VEGWMBEDSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.63α = 90
b = 79.79β = 92.48
c = 98.41γ = 90
Software Package:
Software NamePurpose
DNAdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-02-19
    Changes: Database references, Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description