4KJU

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1021/jm400732v
  • Primary Citation of Related Structures:  

  • 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 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
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase XIAP
A, C
86Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
1RH
Query on 1RH

Download SDF File 
Download CCD File 
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1RHIC50: 6 - 24500 nM (97) BINDINGDB
1RHIC50: 6 nM BINDINGMOAD
1RHIC50: 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 = 75.667α = 90.00
b = 75.667β = 90.00
c = 109.105γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
CCP4model building
CCP4phasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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