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 
  • R-Value Observed: 0.214 

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
  • Structures With Same Primary Citation

  • 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): 16 
Gene Names: BRAFBRAF1RAFB1
EC: 2.7.11.1
Find proteins for P15056 (Homo sapiens)
Go to UniProtKB:  P15056
NIH Common Fund Data Resources
PHAROS  P15056
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
032
Query on 032

Download CCD File 
A
N-(3-{[5-(4-chlorophenyl)-1H-pyrrolo[2,3-b]pyridin-3-yl]carbonyl}-2,4-difluorophenyl)propane-1-sulfonamide
C23 H18 Cl F2 N3 O3 S
GPXBXXGIAQBQNI-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
032IC50:  33   nM  BindingDB
032IC50:  34   nM  BindingDB
032IC50:  33000   nM  BindingDB
032IC50:  119   nM  BindingDB
032IC50:  31   nM  BindingDB
032IC50:  6.900000095367432   nM  BindingDB
32IC50 :  31   nM  PDBBind
032IC50:  150   nM  BindingDB
032EC50:  601   nM  BindingDB
032EC50:  2290   nM  BindingDB
032IC50:  4   nM  BindingDB
032IC50:  17   nM  BindingDB
032IC50:  260   nM  BindingDB
032IC50:  59   nM  BindingDB
032IC50:  6.099999904632568   nM  BindingDB
032IC50:  20   nM  BindingDB
032EC50:  794   nM  BindingDB
032IC50:  21   nM  BindingDB
032IC50:  280   nM  BindingDB
032IC50:  1140   nM  BindingDB
032IC50:  100   nM  BindingDB
032IC50:  23   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.77α = 90
b = 104.424β = 90
c = 110.128γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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