Crystal structure of c-raf (raf-1)

Experimental Data Snapshot

  • Resolution: 4.00 Å
  • R-Value Free: 0.364 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.283 

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RAF inhibitors prime wild-type RAF to activate the MAPK pathway and enhance growth.

Hatzivassiliou, G.Song, K.Yen, I.Brandhuber, B.J.Anderson, D.J.Alvarado, R.Ludlam, M.J.Stokoe, D.Gloor, S.L.Vigers, G.Morales, T.Aliagas, I.Liu, B.Sideris, S.Hoeflich, K.P.Jaiswal, B.S.Seshagiri, S.Koeppen, H.Belvin, M.Friedman, L.S.Malek, S.

(2010) Nature 464: 431-435

  • DOI: https://doi.org/10.1038/nature08833
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Activating mutations in KRAS and BRAF are found in more than 30% of all human tumours and 40% of melanoma, respectively, thus targeting this pathway could have broad therapeutic effects. Small molecule ATP-competitive RAF kinase inhibitors have potent antitumour effects on mutant BRAF(V600E) tumours but, in contrast to mitogen-activated protein kinase kinase (MEK) inhibitors, are not potent against RAS mutant tumour models, despite RAF functioning as a key effector downstream of RAS and upstream of MEK. Here we show that ATP-competitive RAF inhibitors have two opposing mechanisms of action depending on the cellular context. In BRAF(V600E) tumours, RAF inhibitors effectively block the mitogen-activated protein kinase (MAPK) signalling pathway and decrease tumour growth. Notably, in KRAS mutant and RAS/RAF wild-type tumours, RAF inhibitors activate the RAF-MEK-ERK pathway in a RAS-dependent manner, thus enhancing tumour growth in some xenograft models. Inhibitor binding activates wild-type RAF isoforms by inducing dimerization, membrane localization and interaction with RAS-GTP. These events occur independently of kinase inhibition and are, instead, linked to direct conformational effects of inhibitors on the RAF kinase domain. On the basis of these findings, we demonstrate that ATP-competitive kinase inhibitors can have opposing functions as inhibitors or activators of signalling pathways, depending on the cellular context. Furthermore, this work provides new insights into the therapeutic use of ATP-competitive RAF inhibitors.

  • Organizational Affiliation

    Genentech, South San Francisco, California 94080, USA. hatzivassiliou.georgia@gene.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RAF proto-oncogene serine/threonine-protein kinase
A, B
307Homo sapiensMutation(s): 0 
Gene Names: RAF1RAF
UniProt & NIH Common Fund Data Resources
Find proteins for P04049 (Homo sapiens)
Explore P04049 
Go to UniProtKB:  P04049
PHAROS:  P04049
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04049
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SM5

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(1E)-5-(1-piperidin-4-yl-3-pyridin-4-yl-1H-pyrazol-4-yl)-2,3-dihydro-1H-inden-1-one oxime
C22 H23 N5 O
Experimental Data & Validation

Experimental Data

  • Resolution: 4.00 Å
  • R-Value Free: 0.364 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.283 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.57α = 90
b = 99.57β = 90
c = 161.422γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description