2RGP

Structure of EGFR in complex with hydrazone, a potent dual inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2RGP/pdb

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


• Deposited: 2007-10-04 Released: 2008-08-26 
• Deposition Author(s): Abad, M.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.268 
• R-Value Work: 0.228 

Starting Model: experimental

Literature

4-Amino-6-arylamino-pyrimidine-5-carbaldehyde hydrazones as potent ErbB-2/EGFR dual kinase inhibitors.

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

(2008) Bioorg Med Chem Lett 18: 4615-4619

• PubMed: 18653333 
• DOI: https://doi.org/10.1016/j.bmcl.2008.07.020
• Primary Citation of Related Structures:  
  2RGP


• PubMed Abstract: 
  

  Members of a novel class of 4-amino-6-arylamino-pyrimidine-5-carbaldehyde hydrazones were identified as potent dual ErbB-2/EGFR kinase inhibitors using concept-guided design approach. These compounds inhibited the growth of ErbB-2 over-expressing human tumor cell lines (BT474, N87, and SK-BR-3) in vitro. Compound 15 emerged as a key lead and showed significant ability to inhibit growth factor-induced receptor phosphorylation in SK-BR-3 cells (IC(50)=54 nM) and cellular proliferation in vitro (IC(50)=14, 58, and 58 nM for BT474, N87, and SK-BR-3 respectively). The X-ray co-crystal structure of EGFR with a close analog (17) was determined and validated our design rationale.

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Organizational Affiliation: 

Johnson & Johnson Pharmaceutical Research and 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: 36.71 kDa 
• Atom Count: 2,417 
• Modelled Residue Count: 284 
• 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
HYZ	D [auth A]	N-[1-(3-fluorobenzyl)-1H-indazol-5-yl]-5-[(piperidin-1-ylamino)methyl]pyrimidine-4,6-diamine C24 H27 F N8 IMHOFYWDXRUQBM-UHFFFAOYSA-N
PO4	B [auth A], C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
HYZ	PDBBind:  2RGP	IC50: 30 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.268 
• R-Value Work: 0.228 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.85	α = 90
b = 68.03	β = 90
c = 103.86	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: 2008-08-26 
Deposition Author(s): Abad, M.C.

Revision History  

• Version 1.0: 2008-08-26
  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