2OPY

Smac mimic bound to BIR3-XIAP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-activity based study of the Smac-binding pocket within the BIR3 domain of XIAP.

Wist, A.D.Gu, L.Riedl, S.J.Shi, Y.McLendon, G.L.

(2007) Bioorg.Med.Chem. 15: 2935-2943

  • DOI: 10.1016/j.bmc.2007.02.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A small series of peptide mimics was designed and synthesized to contain a heterocyclic ring in place of the potentially labile N-terminal peptide bond of the tetrapeptide containing the Smac-XIAP-binding motif. Two Smac mimics were shown to bind to ...

    A small series of peptide mimics was designed and synthesized to contain a heterocyclic ring in place of the potentially labile N-terminal peptide bond of the tetrapeptide containing the Smac-XIAP-binding motif. Two Smac mimics were shown to bind to the BIR3 domain of XIAP with moderate affinity and one displayed increased activity in cells relative to the Smac peptides. The structures of BIR3-XIAP in complex with a Smac peptide and a peptide mimic were solved and analyzed to elucidate the structure-activity relationship surrounding the Smac-binding domain within BIR3-XIAP.


    Organizational Affiliation

    Department of Chemistry, Princeton University, Princeton, NJ 08544, USA. aislyn.wist@mssm.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Baculoviral IAP repeat-containing protein 4
A
106Homo sapiensMutation(s): 0 
Gene Names: XIAP (API3, BIRC4, IAP3)
EC: 2.3.2.27
Find proteins for P98170 (Homo sapiens)
Go to Gene View: XIAP
Go to UniProtKB:  P98170
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CO9
Query on CO9

Download SDF File 
Download CCD File 
A
1-({2-[(1S)-1-AMINOETHYL]-1,3-OXAZOL-4-YL}CARBONYL)-L-PROLYL-L-TRYPTOPHAN
C22 H25 N5 O5
FBRCDLGEWAXPMI-IWEFOYFVSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CO9Kd: 30000 nM (100) BINDINGDB
CO9Kd: 30000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.213 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 71.200α = 90.00
b = 71.200β = 90.00
c = 105.100γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASESphasing
DENZOdata reduction
PHASERphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance