3ETA | pdb_00003eta

Kinase domain of insulin receptor complexed with a pyrrolo pyridine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3ETA/pdb

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


• Deposited: 2008-10-07 Released: 2009-05-26 
• Deposition Author(s): Patnaik, S., Stevens, K., Gerding, R., Deanda, F., Shotwell, B., Tang, J., Hamajima, T., Nakamura, H., Leesnitzer, A., Hassell, A., Shewchuk, L., Kumar, R., Lei, H., Chamberlain, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.232 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Discovery of 3,5-disubstituted-1H-pyrrolo[2,3-b]pyridines as potent inhibitors of the insulin-like growth factor-1 receptor (IGF-1R) tyrosine kinase.

Patnaik, S., Stevens, K.L., Gerding, R., Deanda, F., Shotwell, J.B., Tang, J., Hamajima, T., Nakamura, H., Leesnitzer, M.A., Hassell, A.M., Shewchuck, L.M., Kumar, R., Lei, H., Chamberlain, S.D.

(2009) Bioorg Med Chem Lett 19: 3136-3140

• PubMed: 19394223 
• DOI: https://doi.org/10.1016/j.bmcl.2008.12.110
• Primary Citation Related Structures: 
  3ETA


• PubMed Abstract: 
  

  Exploration of the SAR around a series of 3,5-disubstituted-1H-pyrrolo[2,3-b]pyridines led to the discovery of novel pyrrolopyridine inhibitors of the IGF-1R tyrosine kinase. Several compounds demonstrated nanomolar potency in enzyme and cellular mechanistic assays.

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Organizational Affiliation: 
• GlaxoSmithKline, Oncology R&D, NC 27709, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 73.36 kDa 
• Atom Count: 5,032 
• Modeled Residue Count: 585 
• Deposited Residue Count: 634 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
insulin receptor, kinase domain	A, B	317	Homo sapiens	Mutation(s): 0  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
351	C [auth A], D [auth B]	1-(3-{5-[4-(aminomethyl)phenyl]-1H-pyrrolo[2,3-b]pyridin-3-yl}phenyl)-3-(2-phenoxyphenyl)urea C33 H27 N5 O2 KSTUYVHCHCYOAB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.232 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.105	α = 90
b = 94.751	β = 90
c = 129.858	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-26 
Deposition Author(s): Patnaik, S., Stevens, K., Gerding, R., Deanda, F., Shotwell, B., Tang, J., Hamajima, T., Nakamura, H., Leesnitzer, A., Hassell, A., Shewchuk, L., Kumar, R., Lei, H., Chamberlain, S.

Revision History  

• Version 1.0: 2009-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description