BRAF Kinase domain b3aC loop deletion mutant in complex with sorafenib

Experimental Data Snapshot

  • Resolution: 2.51 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report

This is version 1.3 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 Bioinformatics & Computational Biology, 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
Serine/threonine-protein kinase B-raf283Homo sapiensMutation(s): 16 
UniProt & NIH Common Fund Data Resources
Find proteins for P15056 (Homo sapiens)
Explore P15056 
Go to UniProtKB:  P15056
PHAROS:  P15056
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15056
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on BAX

Download Ideal Coordinates CCD File 
C21 H16 Cl F3 N4 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
BAX BindingDB:  5HI2 Ki: min: 22, max: 38 (nM) from 2 assay(s)
Kd: min: 54, max: 540 (nM) from 4 assay(s)
IC50: min: 4.4, max: 7300 (nM) from 27 assay(s)
EC50: 3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.51 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.191 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.625α = 90
b = 114.92β = 90
c = 101.544γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History 

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: 2016-08-03
    Changes: Structure summary
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description