Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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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: 36238.61 
• Atom Count: 2256 
• Residue Count: 314 
• Unique protein chains: 1

2X2L

Crystal Structure of phosphorylated RET tyrosine kinase domain with inhibitor

• DOI: 10.2210/pdb2X2L/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• 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 Å
• R-Value Free: 0.269 
• R-Value Work: 0.211 

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:  
  2X2M, 2X2K


• 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
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
Find proteins for P07949 (Homo sapiens) Go to Gene View: RET Go to UniProtKB:  P07949

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
FMT	A	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
X2L	A	(3Z)-5-AMINO-3-[(4-METHOXYPHENYL)METHYLIDENE]-1,3-DIHYDRO-2H-INDOL-2-ONE C16 H14 N2 O2 DYCBCUFDDRQCID-ZSOIEALJSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
X2L	IC50: 5300 - 63000 nM (99) BINDINGDB
X2L	IC50: 5300 nM BINDINGMOAD
X2L	IC50: 5300 nM PDBBIND

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length (Å)	Angle (°)
a = 71.999	α = 90.00
b = 70.685	β = 110.35
c = 71.573	γ = 90.00

Software Package:

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

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