EGFR kinase domain mutant "TMLR" with a pyrazolopyrimidine inhibitor

Experimental Data Snapshot

  • Resolution: 2.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1016/j.ccell.2016.02.010
  • Primary Citation of Related Structures:  
    5HI2, 5HIB, 5HIC, 5HID, 5HIE

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor331Homo sapiensMutation(s): 5 
UniProt & NIH Common Fund Data Resources
Find proteins for P00533 (Homo sapiens)
Explore P00533 
Go to UniProtKB:  P00533
PHAROS:  P00533
GTEx:  ENSG00000146648 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00533
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 63M

Download Ideal Coordinates CCD File 
B [auth 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
Experimental Data & Validation

Experimental Data

  • Resolution: 2.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.357α = 90
b = 146.357β = 90
c = 146.357γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-04-20
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations