5AMN | pdb_00005amn

The Discovery of 2-Substituted Phenol Quinazolines as Potent and Selective RET Kinase Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 
    0.237 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

The discovery of 2-substituted phenol quinazolines as potent RET kinase inhibitors with improved KDR selectivity.

Newton, R.Bowler, K.A.Burns, E.M.Chapman, P.J.Fairweather, E.E.Fritzl, S.J.R.Goldberg, K.M.Hamilton, N.M.Holt, S.V.Hopkins, G.V.Jones, S.D.Jordan, A.M.Lyons, A.J.Nikki March, H.McDonald, N.Q.Maguire, L.A.Mould, D.P.Purkiss, A.G.Small, H.F.Stowell, A.I.J.Thomson, G.J.Waddell, I.D.Waszkowycz, B.Watson, A.J.Ogilvie, D.J.

(2016) Eur J Med Chem 112: 20-32

  • DOI: https://doi.org/10.1016/j.ejmech.2016.01.039
  • Primary Citation Related Structures: 
    5AMN

  • PubMed Abstract: 

    Deregulation of the receptor tyrosine kinase RET has been implicated in medullary thyroid cancer, a small percentage of lung adenocarcinomas, endocrine-resistant breast cancer and pancreatic cancer. There are several clinically approved multi-kinase inhibitors that target RET as a secondary pharmacology but additional activities, most notably inhibition of KDR, lead to dose-limiting toxicities. There is, therefore, a clinical need for more specific RET kinase inhibitors. Herein we report our efforts towards identifying a potent and selective RET inhibitor using vandetanib 1 as the starting point for structure-based drug design. Phenolic anilinoquinazolines exemplified by 6 showed improved affinities towards RET but, unsurprisingly, suffered from high metabolic clearance. Efforts to mitigate the metabolic liability of the phenol led to the discovery that a flanking substituent not only improved the hepatocyte stability, but could also impart a significant gain in selectivity. This culminated in the identification of 36; a potent RET inhibitor with much improved selectivity against KDR.


  • Organizational Affiliation
    • Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK. Electronic address: rebecca.newton@cruk.manchester.ac.uk.

Macromolecule Content 

  • Total Structure Weight: 34.97 kDa 
  • Atom Count: 2,310 
  • Modeled Residue Count: 289 
  • Deposited Residue Count: 299 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET299Homo sapiensMutation(s): 0 
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07949 (Homo sapiens)
Explore P07949 
Go to UniProtKB:  P07949
PHAROS:  P07949
GTEx:  ENSG00000165731 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07949
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DTQ

Query on DTQ



Download:Ideal Coordinates CCD File
B [auth A]4-[3-HYDROXYANILINO]-6,7-DIMETHOXYQUINAZOLINE
C16 H15 N3 O3
BNDYIYYKEIXHNK-UHFFFAOYSA-N
FMT

Query on FMT



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Binding Affinity Annotations 
IDSourceBinding Affinity
DTQ BindingDB:  5AMN IC50: min: 4.5, max: 380 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free:  0.237 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.57α = 90
b = 50.57β = 90
c = 242.84γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-17
    Type: Initial release
  • Version 1.1: 2016-03-02
    Changes: Database references
  • Version 1.2: 2018-02-28
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary