4XV2

B-Raf Kinase V600E oncogenic mutant in complex with Dabrafenib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

RAF inhibitors that evade paradoxical MAPK pathway activation.

Zhang, C.Spevak, W.Zhang, Y.Burton, E.A.Ma, Y.Habets, G.Zhang, J.Lin, J.Ewing, T.Matusow, B.Tsang, G.Marimuthu, A.Cho, H.Wu, G.Wang, W.Fong, D.Nguyen, H.Shi, S.Womack, P.Nespi, M.Shellooe, R.Carias, H.Powell, B.Light, E.Sanftner, L.Walters, J.Tsai, J.West, B.L.Visor, G.Rezaei, H.Lin, P.S.Nolop, K.Ibrahim, P.N.Hirth, P.Bollag, G.

(2015) Nature 526: 583-586

  • DOI: 10.1038/nature14982
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Oncogenic activation of BRAF fuels cancer growth by constitutively promoting RAS-independent mitogen-activated protein kinase (MAPK) pathway signalling. Accordingly, RAF inhibitors have brought substantially improved personalized treatment of metasta ...

    Oncogenic activation of BRAF fuels cancer growth by constitutively promoting RAS-independent mitogen-activated protein kinase (MAPK) pathway signalling. Accordingly, RAF inhibitors have brought substantially improved personalized treatment of metastatic melanoma. However, these targeted agents have also revealed an unexpected consequence: stimulated growth of certain cancers. Structurally diverse ATP-competitive RAF inhibitors can either inhibit or paradoxically activate the MAPK pathway, depending whether activation is by BRAF mutation or by an upstream event, such as RAS mutation or receptor tyrosine kinase activation. Here we have identified next-generation RAF inhibitors (dubbed 'paradox breakers') that suppress mutant BRAF cells without activating the MAPK pathway in cells bearing upstream activation. In cells that express the same HRAS mutation prevalent in squamous tumours from patients treated with RAF inhibitors, the first-generation RAF inhibitor vemurafenib stimulated in vitro and in vivo growth and induced expression of MAPK pathway response genes; by contrast the paradox breakers PLX7904 and PLX8394 had no effect. Paradox breakers also overcame several known mechanisms of resistance to first-generation RAF inhibitors. Dissociating MAPK pathway inhibition from paradoxical activation might yield both improved safety and more durable efficacy than first-generation RAF inhibitors, a concept currently undergoing human clinical evaluation with PLX8394.


    Organizational Affiliation

    Plexxikon Inc., 91 Bolivar Drive, Berkeley, California 94710, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase B-raf
A, B
292Homo sapiensMutation(s): 12 
Gene Names: BRAF (BRAF1, RAFB1)
EC: 2.7.11.1
Find proteins for P15056 (Homo sapiens)
Go to Gene View: BRAF
Go to UniProtKB:  P15056
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P06
Query on P06

Download SDF File 
Download CCD File 
A, B
Dabrafenib
N-{3-[5-(2-aminopyrimidin-4-yl)-2-tert-butyl-1,3-thiazol-4-yl]-2-fluorophenyl}-2,6-difluorobenzenesulfonamide
C23 H20 F3 N5 O2 S2
BFSMGDJOXZAERB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
P06EC50: 529 nM (93) BINDINGDB
P06IC50: 0.4 - 11 nM (93) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.689α = 90.00
b = 105.666β = 90.00
c = 109.731γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
MOLREPphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-01-26 
  • Released Date: 2015-10-28 
  • Deposition Author(s): zhang, Y., zhang, c.

Revision History 

  • Version 1.0: 2015-10-28
    Type: Initial release
  • Version 1.1: 2015-11-04
    Type: Database references