X-ray structure of EGFR in complex with oxime inhibitor

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.241 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1016/j.bmcl.2008.05.024
  • Primary Citation of Related Structures:  

  • 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 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor315Homo sapiensMutation(s): 0 
Gene Names: EGFRERBB1
UniProt & NIH Common Fund Data Resources
Find proteins for P00533 (Homo sapiens)
Explore P00533 
Go to UniProtKB:  P00533
PHAROS:  P00533
GTEx:  ENSG00000146648 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00533
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on POX

Download Ideal Coordinates CCD File 
D [auth A]4-amino-6-{[1-(3-fluorobenzyl)-1H-indazol-5-yl]amino}pyrimidine-5-carbaldehyde O-(2-methoxyethyl)oxime
C22 H22 F N7 O2
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
O4 P
Binding Affinity Annotations 
IDSourceBinding Affinity
POX Binding MOAD:  3BEL IC50: 14 (nM) from 1 assay(s)
PDBBind:  3BEL IC50: 14 (nM) from 1 assay(s)
BindingDB:  3BEL IC50: 14 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 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
b = 67.686β = 90
c = 103.252γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description