Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 36.24 kDa 
• Atom Count: 2327 
• Modelled Residue Count: 288 
• Deposited Residue Count: 314 
• Unique protein chains: 1

2X2L

Crystal Structure of phosphorylated RET tyrosine kinase domain with inhibitor

• PDB DOI: 10.2210/pdb2X2L/pdb

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


• Deposited: 2010-01-13 Released: 2010-02-09 
• Deposition Author(s): Knowles, P.P., Murray-Rust, J., Kjaer, S., McDonald, N.Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.269 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 

Literature

Synthesis, structure-activity relationship and crystallographic studies of 3-substituted indolin-2-one RET inhibitors.

Mologni, L., Rostagno, R., Brussolo, S., Knowles, P.P., Kjaer, S., Murray-Rust, J., Rosso, E., Zambon, A., Scapozza, L., McDonald, N.Q., Lucchini, V., Gambacorti-Passerini, C.

(2010) Bioorg Med Chem 18: 1482-1496

• PubMed: 20117004 
• DOI: 10.1016/j.bmc.2010.01.011
• Primary Citation of Related Structures:  
  2X2K, 2X2L, 2X2M


• PubMed Abstract: 
  

The synthesis, structure-activity relationships (SAR) and structural data of a series of indolin-2-one inhibitors of RET tyrosine kinase are described. These compounds were designed to explore the available space around the indolinone scaffold within RET active site. Several substitutions at different positions were tested and biochemical data were used to draw a molecular model of steric and electrostatic interactions, which can be applied to design more potent and selective RET inhibitors. The crystal structures of RET kinase domain in complex with three inhibitors were solved. All three compounds bound in the ATP pocket and formed two hydrogen bonds with the kinase hinge region. Crystallographic analysis confirmed predictions from molecular modelling and helped refine SAR results. These data provide important information for the development of indolinone inhibitors for the treatment of RET-driven cancers.

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Organizational Affiliation: 

Department of Clinical Medicine and Prevention, University of Milano-Bicocca, Monza, Italy. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET	A	314	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 GTEx:  ENSG00000165731

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X2L	F [auth A]	(3Z)-5-AMINO-3-[(4-METHOXYPHENYL)METHYLIDENE]-1,3-DIHYDRO-2H-INDOL-2-ONE C16 H14 N2 O2 DYCBCUFDDRQCID-ZSOIEALJSA-N
FMT	B [auth A], C [auth A], D [auth A], E [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
X2L	BindingDB:  2X2L	IC50: min: 5300, max: 6.30e+4 (nM) from 2 assay(s)
	PDBBind:  2X2L	IC50: 5300 (nM) from 1 assay(s)
	Binding MOAD:  2X2L	IC50: 5300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.269 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.999	α = 90
b = 70.685	β = 110.35
c = 71.573	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-01-13 
• Released Date: 2010-02-09 
Deposition Author(s): Knowles, P.P., Murray-Rust, J., Kjaer, S., McDonald, N.Q.

Revision History  

• Version 1.0: 2010-02-09
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-02-28
  Changes: Database references
• Version 1.4: 2019-01-30
  Changes: Data collection, Experimental preparation
• Version 1.5: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation