2OJ9

Structure of IGF-1R kinase domain complexed with a benzimidazole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2OJ9/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2007-01-12 Released: 2007-05-01 
• Deposition Author(s): Sack, J.S., Jacobson, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.276 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 

Literature

Discovery and initial SAR of 3-(1H-benzo[d]imidazol-2-yl)pyridin-2(1H)-ones as inhibitors of insulin-like growth factor 1-receptor (IGF-1R).

Velaparthi, U., Wittman, M., Liu, P., Stoffan, K., Zimmermann, K., Sang, X., Carboni, J., Li, A., Attar, R., Gottardis, M., Greer, A., Chang, C.Y., Jacobsen, B.L., Sack, J.S., Sun, Y., Langley, D.R., Balasubramanian, B., Vyas, D.

(2007) Bioorg Med Chem Lett 17: 2317-2321

• PubMed: 17317169 
• DOI: https://doi.org/10.1016/j.bmcl.2007.01.102
• Primary Citation of Related Structures:  
  2OJ9


• PubMed Abstract: 
  

  The discovery and synthesis of 3-(1H-benzo[d]imidazol-2-yl)pyridin-2(1H)-one inhibitors of insulin-like growth factor 1-receptor (IGF-1R) are presented. Installing amine containing side chains at the 4-position of pyridone ring significantly improved the enzyme potency. SAR and biological activity of these compounds is presented.

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Organizational Affiliation: 

Department of Discovery Chemistry, Bristol-Myers Squibb Pharmaceutical Research Institute, 5 Research Parkway, Wallingford, CT 06492, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.44 kDa 
• Atom Count: 2,592 
• Modelled Residue Count: 295 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-like growth factor 1 receptor precursor (EC 2.7.10.1) (Insulin-like growth factor I receptor) (IGF-I receptor) (CD221 antigen)	A	307	Homo sapiens	Mutation(s): 0  Gene Names: IGF1R EC: 2.7.1.112 (PDB Primary Data), 2.7.10.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P08069 (Homo sapiens) Explore P08069  Go to UniProtKB:  P08069
PHAROS:  P08069 GTEx:  ENSG00000140443

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMI	B [auth A]	3-[5-(1H-IMIDAZOL-1-YL)-7-METHYL-1H-BENZIMIDAZOL-2-YL]-4-[(PYRIDIN-2-YLMETHYL)AMINO]PYRIDIN-2(1H)-ONE C22 H19 N7 O GLTRPHMPCVLOJS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BMI	PDBBind:  2OJ9	IC50: 390 (nM) from 1 assay(s)
	BindingDB:  2OJ9	IC50: 390 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.276 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.271	α = 90
b = 44.289	β = 99.05
c = 65.744	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
BUSTER-TNT	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-01 
Deposition Author(s): Sack, J.S., Jacobson, B.L.

Revision History  

• Version 1.0: 2007-05-01
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations