Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 13.85 kDa 
• Atom Count: 858 
• Modelled Residue Count: 97 
• Deposited Residue Count: 116 
• Unique protein chains: 1

2JK7

XIAP BIR3 bound to a Smac Mimetic

• PDB DOI: 10.2210/pdb2JK7/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-08-21 Released: 2008-11-04 
• Deposition Author(s): Saito, N.G., Meagher, J.L., Stuckey, J.A.

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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 

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

• PubMed: 18954041 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4	A	116	Homo sapiens	Mutation(s): 0  Gene Names: XIAP, API3, BIRC4, IAP3 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BI6	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
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BI6	PDBBind:  2JK7	Ki: 67 (nM) from 1 assay(s)

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 = 115.76	α = 90
b = 115.76	β = 90
c = 61.79	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-08-21 
• Released Date: 2008-11-04 
Deposition Author(s): Saito, N.G., Meagher, J.L., Stuckey, J.A.

Revision History  

• 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