6XFP

Crystal Structure of BRAF kinase domain bound to Belvarafenib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

ARAF mutations confer resistance to the RAF inhibitor belvarafenib in melanoma.

Yen, I.Shanahan, F.Lee, J.Hong, Y.S.Shin, S.J.Moore, A.R.Sudhamsu, J.Chang, M.T.Bae, I.Dela Cruz, D.Hunsaker, T.Klijn, C.Liau, N.P.D.Lin, E.Martin, S.E.Modrusan, Z.Piskol, R.Segal, E.Venkatanarayan, A.Ye, X.Yin, J.Zhang, L.Kim, J.S.Lim, H.S.Kim, K.P.Kim, Y.J.Han, H.S.Lee, S.J.Kim, S.T.Jung, M.Hong, Y.H.Noh, Y.S.Choi, M.Han, O.Nowicka, M.Srinivasan, S.Yan, Y.Kim, T.W.Malek, S.

(2021) Nature 594: 418-423

  • DOI: https://doi.org/10.1038/s41586-021-03515-1
  • Primary Citation of Related Structures:  
    6XFP

  • PubMed Abstract: 

    Although RAF monomer inhibitors (type I.5, BRAF(V600)) are clinically approved for the treatment of BRAF V600 -mutant melanoma, they are ineffective in non-BRAF V600 mutant cells 1-3 . Belvarafenib is a potent and selective RAF dimer (type II) inhibitor that exhibits clinical activity in patients with BRAF V600E - and NRAS-mutant melanomas. Here we report the first-in-human phase I study investigating the maximum tolerated dose, and assessing the safety and preliminary efficacy of belvarafenib in BRAF V600E - and RAS-mutated advanced solid tumours (NCT02405065, NCT03118817). By generating belvarafenib-resistant NRAS-mutant melanoma cells and analysing circulating tumour DNA from patients treated with belvarafenib, we identified new recurrent mutations in ARAF within the kinase domain. ARAF mutants conferred resistance to belvarafenib in both a dimer- and a kinase activity-dependent manner. Belvarafenib induced ARAF mutant dimers, and dimers containing mutant ARAF were active in the presence of inhibitor. ARAF mutations may serve as a general resistance mechanism for RAF dimer inhibitors as the mutants exhibit reduced sensitivity to a panel of type II RAF inhibitors. The combination of RAF plus MEK inhibition may be used to delay ARAF-driven resistance and suggests a rational combination for clinical use. Together, our findings reveal specific and compensatory functions for the ARAF isoform and implicate ARAF mutations as a driver of resistance to RAF dimer inhibitors.


  • Organizational Affiliation

    Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-raf288Homo sapiensMutation(s): 0 
Gene Names: BRAF
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
GTEx:  ENSG00000157764 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15056
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V1Y
Query on V1Y

Download Ideal Coordinates CCD File 
B [auth A]4-amino-N-{1-[(3-chloro-2-fluorophenyl)amino]-6-methylisoquinolin-5-yl}thieno[3,2-d]pyrimidine-7-carboxamide
C23 H16 Cl F N6 O S
KVCQTKNUUQOELD-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.793α = 90
b = 119.563β = 90
c = 103.934γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-10
    Type: Initial release
  • Version 1.1: 2021-06-09
    Changes: Database references
  • Version 1.2: 2021-06-30
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description