3HL5

Crystal structure of XIAP BIR3 with CS3

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Antagonism of c-IAP and XIAP proteins is required for efficient induction of cell death by small-molecule IAP antagonists.

Ndubaku, C., Varfolomeev, E., Wang, L., Zobel, K., Lau, K., Elliott, L.O., Maurer, B., Fedorova, A.V., Dynek, J.N., Koehler, M., Hymowitz, S.G., Tsui, V., Deshayes, K., Fairbrother, W.J., Flygare, J.A., Vucic, D.

(2009) Acs Chem.Biol. 4: 557-566

  • DOI: 10.1021/cb900083m

  • PubMed Abstract: 

    • The inhibitor of apoptosis (IAP) proteins are critical regulators of cancer cell survival, which makes them attractive targets for therapeutic intervention in cancers. Herein, we describe the structure-based design of IAP antagonists with high affini ...

    The inhibitor of apoptosis (IAP) proteins are critical regulators of cancer cell survival, which makes them attractive targets for therapeutic intervention in cancers. Herein, we describe the structure-based design of IAP antagonists with high affinities and selectivity (>2000-fold) for c-IAP1 over XIAP and their functional characterization as activators of apoptosis in tumor cells. Although capable of inducing cell death and preventing clonogenic survival, c-IAP-selective antagonists are significantly less potent in promoting apoptosis when compared to pan-selective compounds. However, both pan-IAP- and c-IAP-selective antagonists stimulate c-IAP1 and c-IAP2 degradation and activation of NF-kappaB pathways with comparable potencies. Therefore, although compounds that specifically target c-IAP1 and c-IAP2 are capable of inducing apoptosis, antagonism of the c-IAP proteins and XIAP is required for efficient induction of cancer cell death by IAP antagonists.

    Organizational Affiliation: 

    Departments of Medicinal Chemistry and Protein Engineering, Genentech, Inc., South San Francisco, CA 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Baculoviral IAP repeat-containing protein 4
A, B
95Homo sapiensMutation(s): 0 
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, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
9JZ
Query on 9JZ
Download SDF File 
Download CCD File 
A, B
(3S)-1-{(2S)-2-cyclohexyl-2-[(N-methyl-L-alanyl)amino]acetyl}-3-methyl-N-(2-pyrimidin-2-ylphenyl)-L-prolinamide
C28 H38 N6 O3
HNXBUVYVPBCESY-WJNSRDFLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9JZKi: 34000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 103.913α = 90.00
b = 39.940β = 100.00
c = 49.929γ = 90.00
Software Package:
Software NamePurpose
BOSdata collection
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2009-05-26 
  • Released Date: 2009-06-16 
  • Deposition Author(s): Hymowitz, S.G.

Revision History 

  • Version 1.0: 2009-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance