3OG7

B-Raf Kinase V600E oncogenic mutant in complex with PLX4032


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma.

Bollag, G.Hirth, P.Tsai, J.Zhang, J.Ibrahim, P.N.Cho, H.Spevak, W.Zhang, C.Zhang, Y.Habets, G.Burton, E.A.Wong, B.Tsang, G.West, B.L.Powell, B.Shellooe, R.Marimuthu, A.Nguyen, H.Zhang, K.Y.Artis, D.R.Schlessinger, J.Su, F.Higgins, B.Iyer, R.D'Andrea, K.Koehler, A.Stumm, M.Lin, P.S.Lee, R.J.Grippo, J.Puzanov, I.Kim, K.B.Ribas, A.McArthur, G.A.Sosman, J.A.Chapman, P.B.Flaherty, K.T.Xu, X.Nathanson, K.L.Nolop, K.

(2010) Nature 467: 596-599

  • DOI: 10.1038/nature09454

  • PubMed Abstract: 
  • B-RAF is the most frequently mutated protein kinase in human cancers. The finding that oncogenic mutations in BRAF are common in melanoma, followed by the demonstration that these tumours are dependent on the RAF/MEK/ERK pathway, offered hope that in ...

    B-RAF is the most frequently mutated protein kinase in human cancers. The finding that oncogenic mutations in BRAF are common in melanoma, followed by the demonstration that these tumours are dependent on the RAF/MEK/ERK pathway, offered hope that inhibition of B-RAF kinase activity could benefit melanoma patients. Herein, we describe the structure-guided discovery of PLX4032 (RG7204), a potent inhibitor of oncogenic B-RAF kinase activity. Preclinical experiments demonstrated that PLX4032 selectively blocked the RAF/MEK/ERK pathway in BRAF mutant cells and caused regression of BRAF mutant xenografts. Toxicology studies confirmed a wide safety margin consistent with the high degree of selectivity, enabling Phase 1 clinical trials using a crystalline formulation of PLX4032 (ref. 5). In a subset of melanoma patients, pathway inhibition was monitored in paired biopsy specimens collected before treatment initiation and following two weeks of treatment. This analysis revealed substantial inhibition of ERK phosphorylation, yet clinical evaluation did not show tumour regressions. At higher drug exposures afforded by a new amorphous drug formulation, greater than 80% inhibition of ERK phosphorylation in the tumours of patients correlated with clinical response. Indeed, the Phase 1 clinical data revealed a remarkably high 81% response rate in metastatic melanoma patients treated at an oral dose of 960 mg twice daily. These data demonstrate that BRAF-mutant melanomas are highly dependent on B-RAF kinase activity.


    Organizational Affiliation

    Plexxikon Inc., 91 Bolivar Drive, Berkeley, California 94710, USA. gbollag@plexxikon.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AKAP9-BRAF fusion protein
A, B
289Homo sapiensMutation(s): 15 
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
032
Query on 032

Download SDF File 
Download CCD File 
A
N-(3-{[5-(4-chlorophenyl)-1H-pyrrolo[2,3-b]pyridin-3-yl]carbonyl}-2,4-difluorophenyl)propane-1-sulfonamide
Vemurafenib, PLX4032
C23 H18 Cl F2 N3 O3 S
GPXBXXGIAQBQNI-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
032IC50: 4 - 1140 nM (93) BINDINGDB
032EC50: 794 - 2290 nM (93) BINDINGDB
32IC50: 31 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.770α = 90.00
b = 104.424β = 90.00
c = 110.128γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
MOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Structure summary
  • Version 1.3: 2018-05-02
    Type: Data collection, Structure summary