5HIC

EGFR kinase domain mutant "TMLR" with a imidazopyridinyl-aminopyrimidine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.189 

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 Discovery Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
63N
Query on 63N

Download SDF File 
Download CCD File 
A
N-{2-[1-(cyclopropylsulfonyl)-1H-pyrazol-4-yl]pyrimidin-4-yl}-1-(propan-2-yl)-1H-imidazo[4,5-c]pyridin-6-amine
C19 H20 N8 O2 S
KFXLXULLMZFVJO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.189 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 146.434α = 90.00
b = 146.434β = 90.00
c = 146.434γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
SCALEPACKdata scaling
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