2OJ9 | pdb_00002oj9

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 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BMIClick on this verticalbar to view details

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 (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 
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 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 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BMIClick on this verticalbar to view details

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