ErbB4 kinase domain complexed with a thienopyrimidine inhibitor

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


6-Ethynylthieno[3,2-d]- and 6-ethynylthieno[2,3-d]pyrimidin-4-anilines as tunable covalent modifiers of ErbB kinases.

Wood, E.R.Shewchuk, L.M.Ellis, B.Brignola, P.Brashear, R.L.Caferro, T.R.Dickerson, S.H.Dickson, H.D.Donaldson, K.H.Gaul, M.Griffin, R.J.Hassell, A.M.Keith, B.Mullin, R.Petrov, K.G.Reno, M.J.Rusnak, D.W.Tadepalli, S.M.Ulrich, J.C.Wagner, C.D.Vanderwall, D.E.Waterson, A.G.Williams, J.D.White, W.L.Uehling, D.E.

(2008) Proc Natl Acad Sci U S A 105: 2773-2778

  • DOI: https://doi.org/10.1073/pnas.0708281105
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Analysis of the x-ray crystal structure of mono-substituted acetylenic thienopyrimidine 6 complexed with the ErbB family enzyme ErbB-4 revealed a covalent bond between the terminal carbon of the acetylene moiety and the sulfhydryl group of Cys-803 at the solvent interface. The identification of this covalent adduct suggested that acetylenic thienopyrimidine 6 and related analogs might also be capable of forming an analogous covalent adduct with EGFR, which has a conserved cysteine (797) near the ATP binding pocket. To test this hypothesis, we treated a truncated, catalytically competent form of EGFR (678-1020) with a structurally related propargylic amine (8). An investigation of the resulting complex by mass spectrometry revealed the formation of a covalent complex of thienopyrimidine 8 with Cys-797 of EGFR. This finding enabled us to readily assess the irreversibility of various inhibitors and also facilitated a structure-activity relationship understanding of the covalent modifying potential and biological activity of a series of acetylenic thienopyrimidine compounds with potent antitumor activity. Several ErbB family enzyme and cell potent 6-ethynyl thienopyrimidine kinase inhibitors were found to form covalent adducts with EGFR.

  • Organizational Affiliation

    Department of Assay Development, GlaxoSmithKline, Research Triangle Park, NC 27709, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor tyrosine-protein kinase erbB-4
A, B
321Homo sapiensMutation(s): 0 
Gene Names: ERBB4HER4
UniProt & NIH Common Fund Data Resources
Find proteins for Q15303 (Homo sapiens)
Explore Q15303 
Go to UniProtKB:  Q15303
PHAROS:  Q15303
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15303
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GW7

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C21 H17 Cl F N3 O S
Binding Affinity Annotations 
IDSourceBinding Affinity
GW7 PDBBind:  2R4B IC50: 66 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.872α = 90
b = 63.872β = 90
c = 163.607γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description