5HIC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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:  
    5HI2, 5HIC, 5HIB, 5HIE, 5HID

  • 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. Electronic address: shivam@gene.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Epidermal growth factor receptorA331Homo sapiensMutation(s): 5 
Gene Names: EGFRERBBERBB1HER1
EC: 2.7.10.1
Find proteins for P00533 (Homo sapiens)
Explore P00533 
Go to UniProtKB:  P00533
NIH Common Fund Data Resources
PHAROS  P00533
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
63N
Query on 63N

Download Ideal Coordinates 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
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.434α = 90
b = 146.434β = 90
c = 146.434γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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
    Changes: Database references