Fragment Derived XIAP inhibitor

Experimental Data Snapshot

  • Resolution: 2.63 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


A Fragment-Derived Clinical Candidate for Antagonism of X-Linked and Cellular Inhibitor of Apoptosis Proteins: 1-(6-[(4-Fluorophenyl)methyl]-5-(hydroxymethyl)-3,3-dimethyl-1 H,2 H,3 H-pyrrolo[3,2- b]pyridin-1-yl)-2-[(2 R,5 R)-5-methyl-2-([(3R)-3-methylmorpholin-4-yl]methyl)piperazin-1-yl]ethan-1-one (ASTX660).

Johnson, C.N.Ahn, J.S.Buck, I.M.Chiarparin, E.Day, J.E.H.Hopkins, A.Howard, S.Lewis, E.J.Martins, V.Millemaggi, A.Munck, J.M.Page, L.W.Peakman, T.Reader, M.Rich, S.J.Saxty, G.Smyth, T.Thompson, N.T.Ward, G.A.Williams, P.A.Wilsher, N.E.Chessari, G.

(2018) J Med Chem 61: 7314-7329

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b00900
  • Primary Citation of Related Structures:  
    6H6Q, 6H6R

  • PubMed Abstract: 

    Inhibitor of apoptosis proteins (IAPs) are promising anticancer targets, given their roles in the evasion of apoptosis. Several peptidomimetic IAP antagonists, with inherent selectivity for cellular IAP (cIAP) over X-linked IAP (XIAP), have been tested in the clinic. A fragment screening approach followed by structure-based optimization has previously been reported that resulted in a low-nanomolar cIAP1 and XIAP antagonist lead molecule with a more balanced cIAP-XIAP profile. We now report the further structure-guided optimization of the lead, with a view to improving the metabolic stability and cardiac safety profile, to give the nonpeptidomimetic antagonist clinical candidate 27 (ASTX660), currently being tested in a phase 1/2 clinical trial (NCT02503423).

  • Organizational Affiliation

    Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase XIAP
A, B
127Homo sapiensMutation(s): 0 
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
FUK (Subject of Investigation/LOI)
Query on FUK

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
C30 H42 F N5 O3
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
FUK BindingDB:  6H6Q IC50: 7.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.63 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.491α = 90
b = 99.491β = 90
c = 107.043γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection
  • Version 1.2: 2018-09-05
    Changes: Data collection, Database references
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references