Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 36.36 kDa 
• Atom Count: 2296 
• Residue Count: 289 
• Unique protein chains: 1

2IVU

Crystal structure of phosphorylated RET tyrosine kinase domain complexed with the inhibitor ZD6474

• DOI: 10.2210/pdb2IVU/pdb

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


• Deposited: 2006-06-16 Released: 2006-08-10 
• Deposition Author(s): Knowles, P.P., Murray-Rust, J., McDonald, N.Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.248 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 

Literature

Structure and chemical inhibition of the RET tyrosine kinase domain.

Knowles, P.P., Murray-Rust, J., Kjaer, S., Scott, R.P., Hanrahan, S., Santoro, M., Ibanez, C.F., McDonald, N.Q.

(2006) J Biol Chem 281: 33577-33587

• PubMed: 16928683 
• DOI: 10.1074/jbc.M605604200
• Primary Citation of Related Structures:  
  2IVV, 2IVU, 2IVT, 2IVS


• PubMed Abstract: 
  

The RET proto-oncogene encodes a receptor tyrosine kinase for the glial cell line-derived neurotrophic factor family of ligands. Loss-of-function mutations in RET are implicated in Hirschsprung disease, whereas activating mutations in RET are found in human cancers, including familial medullar thyroid carcinoma and multiple endocrine neoplasias 2A and 2B. We report here the biochemical characterization of the human RET tyrosine kinase domain and the structure determination of the non-phosphorylated and phosphorylated forms. Both structures adopt the same active kinase conformation competent to bind ATP and substrate and have a pre-organized activation loop conformation that is independent of phosphorylation status. In agreement with the structural data, enzyme kinetic data show that autophosphorylation produces only a modest increase in activity. Longer forms of RET containing the juxtamembrane domain and C-terminal tail exhibited similar kinetic behavior, implying that there is no cis-inhibitory mechanism within the RET intracellular domain. Our results suggest the existence of alternative inhibitory mechanisms, possibly in trans, for the autoregulation of RET kinase activity. We also present the structures of the RET tyrosine kinase domain bound to two inhibitors, the pyrazolopyrimidine PP1 and the clinically relevant 4-anilinoquinazoline ZD6474. These structures explain why certain multiple endocrine neoplasia 2-associated RET mutants found in patients are resistant to inhibition and form the basis for design of more effective inhibitors.

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Organizational Affiliation: 

Structural Biology Laboratory, London Research Institute, Cancer Research UK, London WC2A 3PX, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET PRECURSOR	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) Explore P07949  Go to UniProtKB:  P07949
NIH Common Fund Data Resources
PHAROS:  P07949 GTEx:  ENSG00000165731

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZD6	A	Vandetanib C22 H24 Br F N4 O2 UHTHHESEBZOYNR-UHFFFAOYSA-N
FMT	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ZD6	IC50:  102   nM  BindingDB
ZD6	Kd:  14   nM  BindingDB
ZD6	IC50:  100   nM  BindingDB
ZD6	IC50:  400   nM  BindingDB
ZD6	IC50:  97   nM  BindingDB
ZD6	Ki:  375   nM  Binding MOAD
ZD6	IC50:  4   nM  BindingDB
ZD6	IC50:  950   nM  BindingDB
ZD6	IC50:  3597   nM  BindingDB
ZD6	Ki :  375   nM  PDBBind
ZD6	IC50:  49   nM  BindingDB
ZD6	Kd:  34   nM  BindingDB
ZD6	Kd:  10000   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.248 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.409	α = 90
b = 71.42	β = 101.23
c = 78.834	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: 2006-06-16 
• Released Date: 2006-08-10 
Deposition Author(s): Knowles, P.P., Murray-Rust, J., McDonald, N.Q.

Revision History 

• Version 1.0: 2006-08-10
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-06-28
  Changes: Data collection
• Version 2.0: 2017-10-25
  Changes: Atomic model, Database references, Structure summary
• Version 2.1: 2018-02-28
  Changes: Database references
• Version 2.2: 2019-01-30
  Changes: Data collection, Experimental preparation
• Version 2.3: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation