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 6H6R | pdb_00006h6r

Fragment Derived XIAP inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 
    0.243 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6H6R

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 15.21 kDa 
  • Atom Count: 1,115 
  • Modeled Residue Count: 107 
  • Deposited Residue Count: 127 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase XIAP127Homo sapiensMutation(s): 0 
Gene Names: XIAP, API3, BIRC4, IAP3
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P98170 (Homo sapiens)
Explore P98170 
Go to UniProtKB:  P98170
PHAROS:  P98170
GTEx:  ENSG00000101966 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP98170
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FUE

Query on FUE



Download:Ideal Coordinates CCD File
D [auth A]2-[[(2~{R},5~{R})-1-[2-[6-[(4-fluorophenyl)methyl]-3,3-dimethyl-2~{H}-pyrrolo[3,2-b]pyridin-1-yl]-2-oxidanylidene-ethyl]-5-methyl-piperazin-2-yl]methyl]-3~{H}-isoindol-1-one
C32 H36 F N5 O2
XYDGOXJJDFKAAT-QFQXNSOFSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
FUE BindingDB:  6H6R IC50: 30 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free:  0.243 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.352α = 90
b = 71.352β = 90
c = 105.569γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
BUSTERphasing

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: 2018-09-05
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references, Derived calculations