5HHW | pdb_00005hhw

Crystal structure of insulin receptor kinase domain in complex with cis-(R)-7-(3-(azetidin-1-ylmethyl)cyclobutyl)-5-(3-((tetrahydro-2H-pyran-2-yl)methoxy)phenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine.

• PDB DOI: https://doi.org/10.2210/pdb5HHW/pdb

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


• Deposited: 2016-01-11 Released: 2016-04-13 
• Deposition Author(s): Scheufler, C., Izaac, A., Stauffer, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.198 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: other

Literature

Identification of a 5-[3-phenyl-(2-cyclic-ether)-methylether]-4-aminopyrrolo[2,3-d]pyrimidine series of IGF-1R inhibitors.

Stauffer, F., Cowan-Jacob, S.W., Scheufler, C., Furet, P.

(2016) Bioorg Med Chem Lett 26: 2065-2067

• PubMed: 26951750 
• DOI: https://doi.org/10.1016/j.bmcl.2016.02.074
• Primary Citation Related Structures: 
  5HHW, 5HZN


• PubMed Abstract: 
  

  We report structure-guided modifications of the benzyloxy substituent of the Insulin-like Growth Factor-1 Receptor (IGF-1R) inhibitor NVP-AEW541. This chemical group has been shown to confer selectivity against other protein kinases but at the expense of a metabolism liability. X-ray crystallography has revealed that the benzyloxy moiety interacts with a lysine cation of the IGF-1R kinase domain via its ether function and its aromatic π-system and is nicely embedded in an induced hydrophobic pocket. We show that 1,4-diethers displaying an adequate hydrophobic and constrained shape are advantageous benzyloxy replacements. A single digit nanomolar inhibitor (compound 20, IC50=8.9 nM) was identified following this approach.

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Organizational Affiliation: 
• Novartis Institutes for Biomedical Research, Basel, Postfach, 4002 Basel, Switzerland. Electronic address: [e-mail].
Novartis Institutes for Biomedical Research, Basel, Postfach, 4002 Basel, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 35.45 kDa 
• Atom Count: 2,800 
• Modeled Residue Count: 306 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin receptor	A	307	Homo sapiens	Mutation(s): 2  Gene Names: INSR EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P06213 (Homo sapiens) Explore P06213  Go to UniProtKB:  P06213
PHAROS:  P06213 GTEx:  ENSG00000171105

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
60O	B [auth A]	7-[3-(azetidin-1-ylmethyl)cyclobutyl]-5-[3-[[(2~{R})-oxan-2-yl]methoxy]phenyl]pyrrolo[2,3-d]pyrimidin-4-amine C26 H33 N5 O2 UTHVKVUADCCITP-KAGYGMCKSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.198 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.92	α = 90
b = 69.16	β = 90
c = 89.86	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-13 
Deposition Author(s): Scheufler, C., Izaac, A., Stauffer, F.

Revision History  

• Version 1.0: 2016-04-13
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Source and taxonomy
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Refinement description