3BEL

X-ray structure of EGFR in complex with oxime inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3BEL/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2007-11-19 Released: 2008-07-01 
• Deposition Author(s): Abad, M.C., Xu, G., Neeper, M.P., Struble, G.T., Gaul, M.D., Connolly, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.281 
• R-Value Work: 0.241 

Starting Model: experimental

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

• PubMed: 18508264 
• DOI: https://doi.org/10.1016/j.bmcl.2008.05.024
• Primary Citation of Related Structures:  
  3BEL


• 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.

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Organizational Affiliation: 

Johnson & Johnson Pharmaceutical Research & Development, Medicinal Chemistry, 8 Clarke Drive, Cranbury, NJ 08512, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.7 kDa 
• Atom Count: 2,318 
• Modelled Residue Count: 280 
• Deposited Residue Count: 315 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	315	Homo sapiens	Mutation(s): 0  Gene Names: EGFR, ERBB1 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00533 (Homo sapiens) Explore P00533  Go to UniProtKB:  P00533
PHAROS:  P00533 GTEx:  ENSG00000146648

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
POX	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 KSGYKTRNRCPDHT-KVSWJAHQSA-N
PO4	B [auth A], C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
POX	PDBBind:  3BEL	IC50: 14 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 45.499	α = 90
b = 67.686	β = 90
c = 103.252	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-01 
Deposition Author(s): Abad, M.C., Xu, G., Neeper, M.P., Struble, G.T., Gaul, M.D., Connolly, P.J.

Revision History  

• 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