4JVG

B-Raf Kinase in Complex with Birb796

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Inhibitors that stabilize a closed RAF kinase domain conformation induce dimerization.

Lavoie, H., Thevakumaran, N., Gavory, G., Li, J.J., Padeganeh, A., Guiral, S., Duchaine, J., Mao, D.Y., Bouvier, M., Sicheri, F., Therrien, M.

(2013) Nat.Chem.Biol. 9: 428-436

  • DOI: 10.1038/nchembio.1257

  • PubMed Abstract: 

    • RAF kinases have a prominent role in cancer. Their mode of activation is complex but critically requires dimerization of their kinase domains. Unexpectedly, several ATP-competitive RAF inhibitors were recently found to promote dimerization and transa ...

    RAF kinases have a prominent role in cancer. Their mode of activation is complex but critically requires dimerization of their kinase domains. Unexpectedly, several ATP-competitive RAF inhibitors were recently found to promote dimerization and transactivation of RAF kinases in a RAS-dependent manner and, as a result, undesirably stimulate RAS/ERK pathway-mediated cell growth. The mechanism by which these inhibitors induce RAF kinase domain dimerization remains unclear. Here we describe bioluminescence resonance energy transfer-based biosensors for the extended RAF family that enable the detection of RAF dimerization in living cells. Notably, we demonstrate the utility of these tools for profiling kinase inhibitors that selectively modulate RAF dimerization and for probing structural determinants of RAF dimerization in vivo. Our findings, which seem generalizable to other kinase families allosterically regulated by kinase domain dimerization, suggest a model whereby ATP-competitive inhibitors mediate RAF dimerization by stabilizing a rigid closed conformation of the kinase domain.

    Organizational Affiliation: 

    Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signalling, Université de Montréal, Montréal, Québec, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase B-raf
B, A, C, D
284Homo sapiensMutation(s): 16 
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
B96
Query on B96
Download SDF File 
Download CCD File 
A, B, C, D
1-(5-TERT-BUTYL-2-P-TOLYL-2H-PYRAZOL-3-YL)-3-[4-(2-MORPHOLIN-4-YL-ETHOXY)-NAPHTHALEN-1-YL]-UREA
C31 H37 N5 O3
MVCOAUNKQVWQHZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B96Kd: 27 - >10000 nM (94) BINDINGDB
B96IC50: 83.4 nM (94) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.232 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.997α = 90.00
b = 120.610β = 90.44
c = 81.714γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
ADSCdata collection
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-07-03
    Type: Database references