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)

Macromolecule Content

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

 5AMN

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

• PDB DOI:  https://doi.org/10.2210/pdb5AMN/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-03-11 Released: 2016-02-17 
• Deposition Author(s): Newton, R., Bowler, K., Burns, E.M., Chapman, P., Fairweather, E., Fritzl, S., Goldberg, K., Hamilton, N.M., Holt, S.V., Hopkins, G.V., Jones, S.D., Jordan, A.M., Lyons, A., McDonald, N.Q., Maguire, L.A., Mould, D.P., Purkiss, A.G., Small, H.F., Stowell, A., Thomson, G.J., Waddell, I.D., Waszkowycz, B., Watson, A.J., Ogilvie, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 0.237 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 

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

• PubMed: 26874741 
• DOI: https://doi.org/10.1016/j.ejmech.2016.01.039
• Primary Citation of 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.

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Organizational Affiliation: 

Cancer Research UK Manchester Institute, Drug Discovery Unit, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, England, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET	A	299	Homo sapiens	Mutation(s): 0  Gene Names: RET, CDHF12, CDHR16, PTC, RET51 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTQ	B [auth A]	4-[3-HYDROXYANILINO]-6,7-DIMETHOXYQUINAZOLINE C16 H15 N3 O3 BNDYIYYKEIXHNK-UHFFFAOYSA-N
FMT	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
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
DTQ	BindingDB:  5AMN	IC50: 4.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 0.237 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.57	α = 90
b = 50.57	β = 90
c = 242.84	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-17 
Deposition Author(s): Newton, R., Bowler, K., Burns, E.M., Chapman, P., Fairweather, E., Fritzl, S., Goldberg, K., Hamilton, N.M., Holt, S.V., Hopkins, G.V., Jones, S.D., Jordan, A.M., Lyons, A., McDonald, N.Q., Maguire, L.A., Mould, D.P., Purkiss, A.G., Small, H.F., Stowell, A., Thomson, G.J., Waddell, I.D., Waszkowycz, B., Watson, A.J., Ogilvie, D.J.

Revision History  

• 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