3BEL

X-ray structure of EGFR in complex with oxime inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of novel 4-amino-6-arylaminopyrimidine-5-carbaldehyde oximes as dual inhibitors of EGFR and ErbB-2 protein tyrosine kinases.

Xu, G.Searle, L.L.Hughes, T.V.Beck, A.K.Connolly, P.J.Abad, M.C.Neeper, M.P.Struble, G.T.Springer, B.A.Emanuel, S.L.Gruninger, R.H.Pandey, N.Adams, M.Moreno-Mazza, S.Fuentes-Pesquera, A.R.Middleton, S.A.Greenberger, L.M.

(2008) Bioorg.Med.Chem.Lett. 18: 3495-3499

  • DOI: 10.1016/j.bmcl.2008.05.024

  • PubMed Abstract: 
  • We herein disclose a novel series of 4-aminopyrimidine-5-carbaldehyde oximes that are potent and selective inhibitors of both EGFR and ErbB-2 tyrosine kinases, with IC(50) values in the nanomolar range. Structure-activity relationship (SAR) studies e ...

    We herein disclose a novel series of 4-aminopyrimidine-5-carbaldehyde oximes that are potent and selective inhibitors of both EGFR and ErbB-2 tyrosine kinases, with IC(50) values in the nanomolar range. Structure-activity relationship (SAR) studies elucidated a critical role for the 4-amino and C-6 arylamino moieties. The X-ray co-crystal structure of EGFR with 37 was determined and validated our design rationale.


    Organizational Affiliation

    Johnson & Johnson Pharmaceutical Research & Development, Medicinal Chemistry, 8 Clarke Drive, Cranbury, NJ 08512, USA. gxu4@prdus.jnj.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Epidermal growth factor receptor
A
315Homo sapiensGene Names: EGFR (ERBB, ERBB1, HER1)
EC: 2.7.10.1
Find proteins for P00533 (Homo sapiens)
Go to Gene View: EGFR
Go to UniProtKB:  P00533
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
POX
Query on POX

Download SDF File 
Download CCD File 
A
4-amino-6-{[1-(3-fluorobenzyl)-1H-indazol-5-yl]amino}pyrimidine-5-carbaldehyde O-(2-methoxyethyl)oxime
C22 H22 F N7 O2
KSGYKTRNRCPDHT-KVSWJAHQSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
POXIC50: 14 nM (100) BINDINGDB
POXIC50: 14 nM BINDINGMOAD
POXIC50: 14 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.241 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.499α = 90.00
b = 67.686β = 90.00
c = 103.252γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
PDB_EXTRACTdata extraction
HKL-2000data collection
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description