B-Raf Kinase in Complex with PLX4720

Experimental Data Snapshot

  • Resolution: 2.57 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.261 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Discovery of a selective inhibitor of oncogenic B-Raf kinase with potent antimelanoma activity

Tsai, J.Lee, J.T.Wang, W.Zhang, J.Cho, H.Mamo, S.Bremer, R.Gillette, S.Kong, J.Haass, N.K.Sproesser, K.Li, L.Smalley, K.S.Fong, D.Zhu, Y.L.Marimuthu, A.Nguyen, H.Lam, B.Liu, J.Cheung, I.Rice, J.Suzuki, Y.Luu, C.Settachatgul, C.Shellooe, R.Cantwell, J.Kim, S.H.Schlessinger, J.Zhang, K.Y.West, B.L.Powell, B.Habets, G.Zhang, C.Ibrahim, P.N.Hirth, P.Artis, D.R.Herlyn, M.Bollag, G.

(2008) Proc Natl Acad Sci U S A 105: 3041-3046

  • DOI: https://doi.org/10.1073/pnas.0711741105
  • Primary Citation of Related Structures:  
    3C4C, 3C4E, 3C4F, 4FK3

  • PubMed Abstract: 

    BRAF(V600E) is the most frequent oncogenic protein kinase mutation known. Furthermore, inhibitors targeting "active" protein kinases have demonstrated significant utility in the therapeutic repertoire against cancer. Therefore, we pursued the development of specific kinase inhibitors targeting B-Raf, and the V600E allele in particular. By using a structure-guided discovery approach, a potent and selective inhibitor of active B-Raf has been discovered. PLX4720, a 7-azaindole derivative that inhibits B-Raf(V600E) with an IC(50) of 13 nM, defines a class of kinase inhibitor with marked selectivity in both biochemical and cellular assays. PLX4720 preferentially inhibits the active B-Raf(V600E) kinase compared with a broad spectrum of other kinases, and potent cytotoxic effects are also exclusive to cells bearing the V600E allele. Consistent with the high degree of selectivity, ERK phosphorylation is potently inhibited by PLX4720 in B-Raf(V600E)-bearing tumor cell lines but not in cells lacking oncogenic B-Raf. In melanoma models, PLX4720 induces cell cycle arrest and apoptosis exclusively in B-Raf(V600E)-positive cells. In B-Raf(V600E)-dependent tumor xenograft models, orally dosed PLX4720 causes significant tumor growth delays, including tumor regressions, without evidence of toxicity. The work described here represents the entire discovery process, from initial identification through structural and biological studies in animal models to a promising therapeutic for testing in cancer patients bearing B-Raf(V600E)-driven tumors.

  • Organizational Affiliation

    Plexxikon, Inc., 91 Bolivar Drive, Berkeley, CA 94710, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B-Raf proto-oncogene serine/threonine-protein kinase
A, B
280Homo sapiensMutation(s): 14 
UniProt & NIH Common Fund Data Resources
Find proteins for P15056 (Homo sapiens)
Explore P15056 
Go to UniProtKB:  P15056
PHAROS:  P15056
GTEx:  ENSG00000157764 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15056
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 324

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C17 H14 Cl F2 N3 O3 S
Binding Affinity Annotations 
IDSourceBinding Affinity
324 BindingDB:  3C4C Ki: 2.6 (nM) from 1 assay(s)
Kd: min: 100, max: 330 (nM) from 2 assay(s)
IC50: min: 13, max: 220 (nM) from 5 assay(s)
PDBBind:  3C4C IC50: 160 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.57 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.261 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.574α = 90
b = 105.502β = 90
c = 110.15γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-02-21
    Changes: Data collection