HER2 Kinase Domain Complexed with TAK-285

Experimental Data Snapshot

  • Resolution: 3.21 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Design and Synthesis of Novel Human Epidermal Growth Factor Receptor 2 (HER2)/Epidermal Growth Factor Receptor (EGFR) Dual Inhibitors Bearing a Pyrrolo[3,2-d]pyrimidine Scaffold.

Ishikawa, T.Seto, M.Banno, H.Kawakita, Y.Oorui, M.Taniguchi, T.Ohta, Y.Tamura, T.Nakayama, A.Miki, H.Kamiguchi, H.Tanaka, T.Habuka, N.Sogabe, S.Yano, J.Aertgeerts, K.Kamiyama, K.

(2011) J Med Chem 54: 8030-8050

  • DOI: https://doi.org/10.1021/jm2008634
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Dual inhibitors of human epidermal growth factor receptor 2 (HER2) and epidermal growth factor receptor (EGFR) have been investigated for breast, lung, gastric, prostate, and other cancers; one, lapatinib, is currently approved for breast cancer. To develop novel HER2/EGFR dual kinase inhibitors, we designed and synthesized pyrrolo[3,2-d]pyrimidine derivatives capable of fitting into the receptors' ATP binding site. Among the prepared compounds, 34e showed potent HER2 and EGFR (HER1) inhibitory activities as well as tumor growth inhibitory activity. The X-ray cocrystal structures of 34e with both HER2 and EGFR demonstrated that 34e interacts with the expected residues in their respective ATP pockets. Furthermore, reflecting its good oral bioavailability, 34e exhibited potent in vivo efficacy in HER2-overexpressing tumor xenograft models. On the basis of these findings, we report 34e (TAK-285) as a promising candidate for clinical development as a novel HER2/EGFR dual kinase inhibitor.

  • Organizational Affiliation

    Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan. Ishikawa_Tomoyasu@takeda.co.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor tyrosine-protein kinase erbB-2
A, B, C, D
338Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P04626 (Homo sapiens)
Explore P04626 
Go to UniProtKB:  P04626
GTEx:  ENSG00000141736 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04626
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 03P

Download Ideal Coordinates CCD File 
E [auth A],
F [auth C]
C26 H25 Cl F3 N5 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
03P PDBBind:  3RCD IC50: 17 (nM) from 1 assay(s)
BindingDB:  3RCD IC50: min: 3, max: 17 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.21 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.542α = 90.42
b = 64.936β = 89.72
c = 92.36γ = 90.35
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-23
    Type: Initial release
  • Version 1.1: 2011-12-14
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description