3QQU | pdb_00003qqu

Cocrystal structure of unphosphorylated igf with pyrimidine 8

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.302 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.273 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.273 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

Discovery of 2,4-bis-arylamino-1,3-pyrimidines as insulin-like growth factor-1 receptor (IGF-1R) inhibitors.

Buchanan, J.L., Newcomb, J.R., Carney, D.P., Chaffee, S.C., Chai, L., Cupples, R., Epstein, L.F., Gallant, P., Gu, Y., Harmange, J.C., Hodge, K., Houk, B.E., Huang, X., Jona, J., Joseph, S., Jun, H.T., Kumar, R., Li, C., Lu, J., Menges, T., Morrison, M.J., Novak, P.M., van der Plas, S., Radinsky, R., Rose, P.E., Sawant, S., Sun, J.R., Surapaneni, S., Turci, S.M., Xu, K., Yanez, E., Zhao, H., Zhu, X.

(2011) Bioorg Med Chem Lett 21: 2394-2399

  • DOI: https://doi.org/10.1016/j.bmcl.2011.02.075
  • Primary Citation Related Structures: 
    3QQU

  • PubMed Abstract: 

    The insulin-like growth factor-1 receptor (IGF-1R) plays an important role in the regulation of cell growth and differentiation, and in protection from apoptosis. IGF-1R has been shown to be an appealing target for the treatment of human cancer. Herein, we report the synthesis, structure-activity relationships (SAR), X-ray cocrystal structure and in vivo tumor study results for a series of 2,4-bis-arylamino-1,3-pyrimidines.

    • Organizational Affiliation: 
    • Department of Medicinal Chemistry, Amgen Inc., 360 Binney Street, Cambridge, MA 02142, USA. john.buchanan@amgen.com

Macromolecule Content 

  • Total Structure Weight: 139.11 kDa 
  • Atom Count: 9,305 
  • Modeled Residue Count: 1,158 
  • Deposited Residue Count: 1,204 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Insulin-like growth factor 1 receptor
A, B, C, D
301Homo sapiensMutation(s): 0 
Gene Names: IGF1R
EC: 2.7.10.1
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
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
01P BindingDB:  3QQU IC50: min: 2.4, max: 8.4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.302 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.273 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.273 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.792α = 65.37
b = 90.931β = 89.42
c = 96.966γ = 84.67
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2011-04-20 
    • Deposition Author(s): Huang, X.

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Structure summary