2JK7

XIAP BIR3 bound to a Smac Mimetic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure-Based Design, Synthesis, Evaluation, and Crystallographic Studies of Conformationally Constrained Smac Mimetics as Inhibitors of the X-Linked Inhibitor of Apoptosis Protein (Xiap).

Sun, H.Stuckey, J.A.Nikolovska-Coleska, Z.Qin, D.Meagher, J.L.Qiu, S.Lu, J.Yang, C.Saito, N.G.Wang, S.

(2008) J Med Chem 51: 7169

  • DOI: 10.1021/jm8006849
  • Primary Citation of Related Structures:  
    2JK7

  • PubMed Abstract: 
  • Small molecules designed to mimic the binding of Smac protein to X-linked inhibitor of apoptosis protein (XIAP) are being pursued as a promising new class of anticancer drugs. Herein, we report the design, synthesis, and comprehensive structure-activity relationship studies of a series of conformationally constrained bicyclic Smac mimetics ...

    Small molecules designed to mimic the binding of Smac protein to X-linked inhibitor of apoptosis protein (XIAP) are being pursued as a promising new class of anticancer drugs. Herein, we report the design, synthesis, and comprehensive structure-activity relationship studies of a series of conformationally constrained bicyclic Smac mimetics. Our studies led to the discovery of a number of highly potent and cell-permeable Smac mimetics and yielded important new insights into their structure-activity relationship for their binding to XIAP and for their activity in inhibition of cancer cell growth. Determination of the crystal structure of one potent Smac mimetic, compound 21, in complex with XIAP BIR3 provides the structural basis for its high-affinity binding to XIAP and for the design of highly potent Smac mimetics.


    Organizational Affiliation

    Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4A116Homo sapiensMutation(s): 0 
Gene Names: XIAPAPI3BIRC4IAP3
EC: 2.3.2.27
Find proteins for P98170 (Homo sapiens)
Explore P98170 
Go to UniProtKB:  P98170
NIH Common Fund Data Resources
PHAROS:  P98170
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BI6
Query on BI6

Download Ideal Coordinates CCD File 
B [auth A](3S,6S,7Z,10AS)-N-(DIPHENYLMETHYL)-6-{[(2S)-2-(METHYLIDENEAMINO)BUTANOYL]AMINO}-5-OXO-1,2,3,5,6,9,10,10A-OCTAHYDROPYRROLO[1,2-A]AZOCINE-3-CARBOXAMIDE
C29 H34 N4 O3
DOJSRSYBMNHTER-QORCZRPOSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BI6Ki :  67   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.76α = 90
b = 115.76β = 90
c = 61.79γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-04
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance