2OJ9

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

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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

    Department of Discovery Chemistry, Bristol-Myers Squibb Pharmaceutical Research Institute, 5 Research Parkway, Wallingford, CT 06492, USA. upender.velaparthi@bms.com


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Insulin-like growth factor 1 receptor precursor (EC 2.7.10.1) (Insulin-like growth factor I receptor) (IGF-I receptor) (CD221 antigen)307Homo sapiensMutation(s): 0 
Gene Names: IGF1R
EC: 2.7.1.112
UniProt & NIH Common Fund Data Resources
Find proteins for P08069 (Homo sapiens)
Explore P08069 
Go to UniProtKB:  P08069
PHAROS:  P08069
GTEx:  ENSG00000140443 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08069
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BMI
Query on BMI
Download Ideal Coordinates CCD File 
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 
IDSourceBinding Affinity
BMI PDBBind:  2OJ9 IC50: 390 (nM) from 1 assay(s)
BindingDB:  2OJ9 IC50: 390 (nM) from 1 assay(s)
Binding MOAD:  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 = 57.271α = 90
b = 44.289β = 99.05
c = 65.744γ = 90
Software Package:
Software NamePurpose
AMoREphasing
BUSTER-TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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