5HIB

EGFR kinase domain mutant "TMLR" with a pyrazolopyrimidine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Activation Mechanism of Oncogenic Deletion Mutations in BRAF, EGFR, and HER2.

Foster, S.A.Whalen, D.M.Ozen, A.Wongchenko, M.J.Yin, J.Yen, I.Schaefer, G.Mayfield, J.D.Chmielecki, J.Stephens, P.J.Albacker, L.A.Yan, Y.Song, K.Hatzivassiliou, G.Eigenbrot, C.Yu, C.Shaw, A.S.Manning, G.Skelton, N.J.Hymowitz, S.G.Malek, S.

(2016) Cancer Cell 29: 477-493

  • DOI: 10.1016/j.ccell.2016.02.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Activating mutations in protein kinases drive many cancers. While how recurring point mutations affect kinase activity has been described, the effect of in-frame deletions is not well understood. We show that oncogenic deletions within the β3-αC loop ...

    Activating mutations in protein kinases drive many cancers. While how recurring point mutations affect kinase activity has been described, the effect of in-frame deletions is not well understood. We show that oncogenic deletions within the β3-αC loop of HER2 and BRAF are analogous to the recurrent EGFR exon 19 deletions. We identify pancreatic carcinomas with BRAF deletions mutually exclusive with KRAS mutations. Crystal structures of BRAF deletions reveal the truncated loop restrains αC in an active "in" conformation, imparting resistance to inhibitors like vemurafenib that bind the αC "out" conformation. Characterization of loop length explains the prevalence of five amino acid deletions in BRAF, EGFR, and HER2 and highlights the importance of this region for kinase activity and inhibitor efficacy.


    Organizational Affiliation

    Department of Bioinformatics & Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Protein Chemistry & Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Discovery Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA; Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Discovery Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Translational Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Cancer Immunology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Discovery Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Oncology Biomarker Development, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Discovery Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA. Electronic address: shivam@gene.com.,Foundation Medicine, 150 Second Street, Cambridge, MA 02141, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Epidermal growth factor receptor
A
331Homo sapiensMutation(s): 5 
Gene Names: EGFR (ERBB, ERBB1, HER1)
EC: 2.7.10.1
Find proteins for P00533 (Homo sapiens)
Go to Gene View: EGFR
Go to UniProtKB:  P00533
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
63M
Query on 63M

Download SDF File 
Download CCD File 
A
N-tert-butyl-5-{[(1-methyl-1H-pyrazol-5-yl)sulfonyl]amino}pyrazolo[1,5-a]pyrimidine-3-carboxamide
C15 H19 N7 O3 S
TXLKGLIVYSFVAR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.195 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 146.357α = 90.00
b = 146.357β = 90.00
c = 146.357γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
HKL-2000data reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-01-11 
  • Released Date: 2016-04-06 
  • Deposition Author(s): Eigenbrot, C., Yu, C.

Revision History 

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-04-20
    Type: Database references