3OG7

B-Raf Kinase V600E oncogenic mutant in complex with PLX4032

• PDB DOI:  https://doi.org/10.2210/pdb3OG7/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-08-16 Released: 2010-09-22 
• Deposition Author(s): Zhang, Y., Zhang, K.Y., Zhang, C.

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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 

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

• PubMed: 20823850 
• DOI: https://doi.org/10.1038/nature09454
• Primary Citation of Related Structures:  
  3OG7


• 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 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.

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Organizational Affiliation: 

Plexxikon Inc., 91 Bolivar Drive, Berkeley, California 94710, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.45 kDa 
• Atom Count: 4,100 
• Modelled Residue Count: 501 
• Deposited Residue Count: 578 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AKAP9-BRAF fusion protein	A, B	289	Homo sapiens	Mutation(s): 16  Gene Names: BRAF, BRAF1, RAFB1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P15056 (Homo sapiens) Explore P15056  Go to UniProtKB:  P15056
PHAROS:  P15056

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
032	C [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
032	BindingDB:  3OG7	Kd: min: 51, max: 58 (nM) from 2 assay(s)
		IC50: min: 4, max: 3.30e+4 (nM) from 30 assay(s)
		EC50: min: 601, max: 2290 (nM) from 3 assay(s)

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 = 50.77	α = 90
b = 104.424	β = 90
c = 110.128	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-22 
Deposition Author(s): Zhang, Y., Zhang, K.Y., Zhang, C.

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