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

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1021/jm400732v
  • Primary Citation of Related Structures:  
    4KJU, 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase XIAPA,
B [auth C]
86Homo sapiensMutation(s): 2 
EC: 6.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for P98170 (Homo sapiens)
Explore P98170 
Go to UniProtKB:  P98170
GTEx:  ENSG00000101966 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP98170
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1RH

Download Ideal Coordinates CCD File 
D [auth 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
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
E [auth C]
Binding Affinity Annotations 
IDSourceBinding Affinity
1RH Binding MOAD:  4KJU IC50: 6 (nM) from 1 assay(s)
BindingDB:  4KJU IC50: min: 6, max: 2.45e+4 (nM) from 3 assay(s)
PDBBind:  4KJU IC50: 6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.667α = 90
b = 75.667β = 90
c = 109.105γ = 90
Software Package:
Software NamePurpose
CCP4model building
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-27
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description