Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 37.81 kDa 
• Atom Count: 2465 
• Modelled Residue Count: 303 
• Deposited Residue Count: 328 
• Unique protein chains: 1

4JQ7

Crystal structure of EGFR kinase domain in complex with compound 2a

• PDB DOI: 10.2210/pdb4JQ7/pdb

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


• Deposited: 2013-03-20 Released: 2013-06-19 
• Deposition Author(s): Peng, Y.H., Wu, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free: 0.237 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 

Literature

Protein Kinase Inhibitor Design by Targeting the Asp-Phe-Gly (DFG) Motif: The Role of the DFG Motif in the Design of Epidermal Growth Factor Receptor Inhibitors

Peng, Y.H., Shiao, H.Y., Tu, C.H., Liu, P.M., Hsu, J.T., Amancha, P.K., Wu, J.S., Coumar, M.S., Chen, C.H., Wang, S.Y., Lin, W.H., Sun, H.Y., Chao, Y.S., Lyu, P.C., Hsieh, H.P., Wu, S.Y.

(2013) J Med Chem 56: 3889-3903

• PubMed: 23611691 
• DOI: 10.1021/jm400072p
• Primary Citation of Related Structures:  
  4JQ7, 4JQ8, 4JR3, 4JRV


• PubMed Abstract: 
  

The Asp-Phe-Gly (DFG) motif plays an important role in the regulation of kinase activity. Structure-based drug design was performed to design compounds able to interact with the DFG motif; epidermal growth factor receptor (EGFR) was selected as an example. Structural insights obtained from the EGFR/2a complex suggested that an extension from the meta-position on the phenyl group (ring-5) would improve interactions with the DFG motif. Indeed, introduction of an N,N-dimethylamino tail resulted in 4b, which showed almost 50-fold improvement in inhibition compared to 2a. Structural studies confirmed this N,N-dimethylamino tail moved toward the DFG motif to form a salt bridge with the side chain of Asp831. That the interactions with the DFG motif greatly contribute to the potency of 4b is strongly evidenced by synthesizing and testing compounds 2a, 3g, and 4f: when the charge interactions are absent, the inhibitory activity decreased significantly.

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Organizational Affiliation: 

Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	328	Homo sapiens	Mutation(s): 0  Gene Names: EGFR, ERBB, ERBB1, HER1 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KJQ	B [auth A]	(2S)-2-[(5,6-diphenylfuro[2,3-d]pyrimidin-4-yl)amino]-2-phenylethanol C26 H21 N3 O2 CCGBAJCQZPJWCS-OAQYLSRUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
KJQ	BindingDB:  4JQ7	IC50: min: 223, max: 1.00e+4 (nM) from 3 assay(s)
	PDBBind:  4JQ7	IC50: 393 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free: 0.237 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.933	α = 90
b = 145.933	β = 90
c = 145.933	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-03-20 
• Released Date: 2013-06-19 
Deposition Author(s): Peng, Y.H., Wu, J.S.

Revision History  

• Version 1.0: 2013-06-19
  Type: Initial release