6JZ0 | pdb_00006jz0

Crystal structure of EGFR kinase domain in complex with compound 78


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 
    0.248 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

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 Related Structures: 
    6JZ0

  • 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.

Macromolecule Content 

  • Total Structure Weight: 37.78 kDa 
  • Atom Count: 2,530 
  • Modeled Residue Count: 311 
  • Deposited Residue Count: 326 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor326Homo sapiensMutation(s): 0 
Gene Names: EGFR
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00533
Sequence Annotations
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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
NQAMTZUVRFRJCZ-VMMYIZNOSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free:  0.248 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
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
PHENIXrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

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