Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20554.72 
• Atom Count: 1330 
• Residue Count: 172 
• Unique protein chains: 1

4KJU

Crystal structure of XIAP-Bir2 with a bound benzodiazepinone inhibitor.

• DOI: 10.2210/pdb4KJU/pdb

• Classification: APOPTOSIS/APOPTOSIS INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 2013-05-03 Released: 2013-11-27 
• Deposition Author(s): Lukacs, C.M., Janson, C.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.213 
• R-Value Work: 0.180 

Literature

Optimization of Benzodiazepinones as Selective Inhibitors of the X-Linked Inhibitor of Apoptosis Protein (XIAP) Second Baculovirus IAP Repeat (BIR2) Domain.

Kester, R.F., Donnell, A.F., Lou, Y., Remiszewski, S.W., Lombardo, L.J., Chen, S., Le, N.T., Lo, J., Moliterni, J.A., Han, X., Hogg, J.H., Liang, W., Michoud, C., Rupert, K.C., Mischke, S., Le, K., Weisel, M., Janson, C.A., Lukacs, C.M., Fretland, A.J., Hong, K., Polonskaia, A., Gao, L., Li, S., Solis, D.S., Aguilar, D., Tardell, C., Dvorozniak, M., Tannu, S., Lee, E.C., Schutt, A.D., Goggin, B.

(2013) J.Med.Chem. 56: 7788-7803

• PubMed: 24093940 
• DOI: 10.1021/jm400732v
• Primary Citation of Related Structures:  
  4KJV


• PubMed Abstract: 
  

The IAPs are key regulators of the apoptotic pathways and are commonly overexpressed in many cancer cells. IAPs contain one to three BIR domains that are crucial for their inhibitory function. The pro-survival properties of XIAP come from binding of the BIR domains to the pro-apoptotic caspases. The BIR3 domain of XIAP binds and inhibits caspase 9, while the BIR2 domain binds and inhibits the terminal caspases 3 and 7. While XIAP BIR3 inhibitors have previously been reported, they also inhibit cIAP1/2 and promote the release of TNFα, potentially limiting their therapeutic utility. This paper will focus on the optimization of selective XIAP BIR2 inhibitors leading to the discovery of highly potent benzodiazepinone 36 (IC50 = 45 nM), which has high levels of selectivity over XIAP BIR3 and cIAP1 BIR2/3 and shows efficacy in a xenograft pharmacodynamic model monitoring caspase activity while not promoting the release of TNFα in vitro.

---

Organizational Affiliation: 

Departments of Discovery Chemistry, ‡Discovery Technologies, §Non-clinical Safety, Early ADME, and ∥Discovery Oncology, Hoffmann-La Roche Inc. , 340 Kingsland Street, Nutley, New Jersey 07110, United States.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
E3 ubiquitin-protein ligase XIAP	A, C	86	Homo sapiens	Mutation(s): 2  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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, C	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
1RH	A	N-{(3S)-5-(4-aminobenzoyl)-1-[(2-methoxynaphthalen-1-yl)methyl]-2-oxo-2,3,4,5-tetrahydro-1H-1,5-benzodiazepin-3-yl}-N~2~-methyl-L-alaninamide C32 H33 N5 O4 BXNIMYHZUMCTGM-FNZWTVRRSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
1RH	IC50: 6 - 24500 nM (97) BINDINGDB
1RH	IC50: 6 nM BINDINGMOAD
1RH	IC50: 6 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.213 
• R-Value Work: 0.180 
• Space Group: I 4 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 75.667	α = 90.00
b = 75.667	β = 90.00
c = 109.105	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
CCP4	model building
CCP4	phasing
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-05-03 
• Released Date: 2013-11-27 
• Deposition Author(s): Lukacs, C.M., Janson, C.A.

Revision History 

• Version 1.0: 2013-11-27
  Type: Initial release
• Version 1.1: 2014-02-05
  Type: Database references
• Version 1.2: 2017-11-15
  Type: Refinement description