5EDR

EGFR kinase (T790M/L858R) with inhibitor compound 27: ~{N}-(1~{H}-indazol-3-yl)-7,7-dimethyl-2-(2-methylpyrazol-3-yl)-5~{H}-furo[3,4-d]pyrimidin-4-amine

• PDB DOI: https://doi.org/10.2210/pdb5EDR/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2015-10-21 Released: 2015-12-02 
• Deposition Author(s): Eigenbrot, C., Yu, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.215 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 

Literature

4-Aminoindazolyl-dihydrofuro[3,4-d]pyrimidines as non-covalent inhibitors of mutant epidermal growth factor receptor tyrosine kinase.

Hanan, E.J., Baumgardner, M., Bryan, M.C., Chen, Y., Eigenbrot, C., Fan, P., Gu, X.H., La, H., Malek, S., Purkey, H.E., Schaefer, G., Schmidt, S., Sideris, S., Yen, I., Yu, C., Heffron, T.P.

(2016) Bioorg Med Chem Lett 26: 534-539

• PubMed: 26639762 
• DOI: https://doi.org/10.1016/j.bmcl.2015.11.078
• Primary Citation of Related Structures:  
  5EDP, 5EDQ, 5EDR


• PubMed Abstract: 
  

  The treatment of epidermal growth factor receptor (EGFR)-driven non-small cell lung cancers with the T790M resistance mutation remains a significant unmet medical need. We report the identification of 4-aminoindazolyl-dihydrofuro[3,4-d]pyrimidines as non-covalent inhibitors of EGFR, with excellent activity against the T790M resistance double mutants and initial single activating mutants. Using an optimization strategy focused on structure-based design and improving PK properties through metabolite identification, we obtained advanced leads with high oral exposure.

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Organizational Affiliation: 

Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States.

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: 37.91 kDa 
• Atom Count: 2,493 
• Modelled Residue Count: 299 
• Deposited Residue Count: 331 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	331	Homo sapiens	Mutation(s): 5  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
5N4	B [auth A]	~{N}-(1~{H}-indazol-3-yl)-7,7-dimethyl-2-(2-methylpyrazol-3-yl)-5~{H}-furo[3,4-d]pyrimidin-4-amine C19 H19 N7 O HMWMAHXTIWOHMD-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5N4	BindingDB:  5EDR	Ki: min: 0.5, max: 34 (nM) from 4 assay(s)
		IC50: 3000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.215 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.8	α = 90
b = 148.8	β = 90
c = 148.8	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-02 
Deposition Author(s): Eigenbrot, C., Yu, C.

Revision History  

• Version 1.0: 2015-12-02
  Type: Initial release
  
• Version 1.1: 2015-12-23
  Changes: Database references
• Version 1.2: 2016-01-20
  Changes: Database references
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references, Derived calculations