Crystal structure of EGFR kinase domain in complex with compound 78

Experimental Data Snapshot

  • Resolution: 2.86 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

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Discovery of a Furanopyrimidine-Based Epidermal Growth Factor Receptor Inhibitor (DBPR112) as a Clinical Candidate for the Treatment of Non-Small Cell Lung Cancer.

Lin, S.Y.Chang Hsu, Y.Peng, Y.H.Ke, Y.Y.Lin, W.H.Sun, H.Y.Shiao, H.Y.Kuo, F.M.Chen, P.Y.Lien, T.W.Chen, C.H.Chu, C.Y.Wang, S.Y.Yeh, K.C.Chen, C.P.Hsu, T.A.Wu, S.Y.Yeh, T.K.Chen, C.T.Hsieh, H.P.

(2019) J Med Chem 62: 10108-10123

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00722
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Epidermal growth factor receptor (EGFR)-targeted therapy in non-small cell lung cancer represents a breakthrough in the field of precision medicine. Previously, we have identified a lead compound, furanopyrimidine 2 , which contains a ( S )-2-phenylglycinol structure as a key fragment to inhibit EGFR. However, compound 2 showed high clearance and poor oral bioavailability in its pharmacokinetics studies. In this work, we optimized compound 2 by scaffold hopping and exploiting the potent inhibitory activity of various warhead groups to obtain a clinical candidate, 78 (DBPR112), which not only displayed a potent inhibitory activity against EGFR L858R/T790M double mutations but also exhibited tenfold potency better than the third-generation inhibitor, osimertinib, against EGFR and HER2 exon 20 insertion mutations. Overall, pharmacokinetic improvement through lead-to-candidate optimization yielded fourfold oral AUC better that afatinib along with F = 41.5%, an encouraging safety profile, and significant antitumor efficacy in in vivo xenograft models. DBPR112 is currently undergoing phase 1 clinical trial in Taiwan.

  • Organizational Affiliation

    Institute of Biotechnology and Pharmaceutical Research , National Health Research Institutes , 35 Keyan Road , Zhunan, Miaoli County 35053 , Taiwan , ROC.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor326Homo sapiensMutation(s): 0 
Gene Names: EGFR
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CKO (Subject of Investigation/LOI)
Query on CKO

Download Ideal Coordinates CCD File 
B [auth A]E-4-(dimethylamino)-N-[3-[4-[[(1S)-2-oxidanyl-1-phenyl-ethyl]amino]-6-phenyl-furo[2,3-d]pyrimidin-5-yl]phenyl]but-2-enamide
C32 H31 N5 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.86 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.124α = 90
b = 145.124β = 90
c = 145.124γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description