2OPY

Smac mimic bound to BIR3-XIAP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.213 
  • R-Value Observed: 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:  
    2OPY, 2OPZ

  • 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 the BIR3 domain of XIAP with moderate affinity and one displayed increased activity in cells relative to the Smac peptides ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Baculoviral IAP repeat-containing protein 4A106Homo sapiensMutation(s): 0 
Gene Names: BIRC4, API3, IAP3, XIAP
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P98170 (Homo sapiens)
Explore P98170 
Go to UniProtKB:  P98170
PHAROS:  P98170
GTEx:  ENSG00000101966 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP98170
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO9
Query on CO9
Download Ideal Coordinates CCD File 
C [auth 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
ZN
Query on ZN
Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
CO9 PDBBind:  2OPY Kd: 3.00e+4 (nM) from 1 assay(s)
BindingDB:  2OPY Kd: 3.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.2α = 90
b = 71.2β = 90
c = 105.1γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHASESphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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