6H6Q

Fragment Derived XIAP inhibitor

• PDB DOI:  https://doi.org/10.2210/pdb6H6Q/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-07-30 Released: 2018-08-22 
• Deposition Author(s): Williams, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 0.275 
• R-Value Work: 0.252 
• R-Value Observed: 0.253 

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

• PubMed: 30091600 
• 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).

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 30.36 kDa 
• Atom Count: 1,962 
• Modelled Residue Count: 209 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase XIAP	A, B	127	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUK (Subject of Investigation/LOI)	D [auth A], F [auth B]	2-[(2~{R},5~{R})-2-[[(3~{R},5~{R})-3,5-dimethylmorpholin-4-yl]methyl]-5-methyl-piperazin-1-yl]-1-[6-[(~{S})-(4-fluorophenyl)-oxidanyl-methyl]-3,3-dimethyl-2~{H}-pyrrolo[3,2-b]pyridin-1-yl]ethanone C30 H42 F N5 O3 MVQVBQBVVYPBCQ-DTRJGPSISA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FUK	BindingDB:  6H6Q	IC50: 7.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 99.491	α = 90
b = 99.491	β = 90
c = 107.043	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Williams, P.A.

Revision History  

• 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