6UUO

Crystal structure of BRAF kinase domain bound to the PROTAC P4B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.265 

wwPDB Validation   3D Report Full Report

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This is version 2.1 of the entry. See complete history


Literature

Functional characterization of a PROTAC directed against BRAF mutant V600E.

Posternak, G.Tang, X.Maisonneuve, P.Jin, T.Lavoie, H.Daou, S.Orlicky, S.Goullet de Rugy, T.Caldwell, L.Chan, K.Aman, A.Prakesch, M.Poda, G.Mader, P.Wong, C.Maier, S.Kitaygorodsky, J.Larsen, B.Colwill, K.Yin, Z.Ceccarelli, D.F.Batey, R.A.Taipale, M.Kurinov, I.Uehling, D.Wrana, J.Durocher, D.Gingras, A.C.Al-Awar, R.Therrien, M.Sicheri, F.

(2020) Nat Chem Biol 16: 1170-1178

  • DOI: https://doi.org/10.1038/s41589-020-0609-7
  • Primary Citation of Related Structures:  
    6UUO

  • PubMed Abstract: 

    The RAF family kinases function in the RAS-ERK pathway to transmit signals from activated RAS to the downstream kinases MEK and ERK. This pathway regulates cell proliferation, differentiation and survival, enabling mutations in RAS and RAF to act as potent drivers of human cancers. Drugs targeting the prevalent oncogenic mutant BRAF(V600E) have shown great efficacy in the clinic, but long-term effectiveness is limited by resistance mechanisms that often exploit the dimerization-dependent process by which RAF kinases are activated. Here, we investigated a proteolysis-targeting chimera (PROTAC) approach to BRAF inhibition. The most effective PROTAC, termed P4B, displayed superior specificity and inhibitory properties relative to non-PROTAC controls in BRAF(V600E) cell lines. In addition, P4B displayed utility in cell lines harboring alternative BRAF mutations that impart resistance to conventional BRAF inhibitors. This work provides a proof of concept for a substitute to conventional chemical inhibition to therapeutically constrain oncogenic BRAF.


  • Organizational Affiliation

    Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-raf
A, B
284Homo sapiensMutation(s): 16 
Gene Names: BRAFBRAF1RAFB1
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QH1 (Subject of Investigation/LOI)
Query on QH1

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
N-(3-{5-[(1-acetylpiperidin-4-yl)(methyl)amino]-3-(pyrimidin-5-yl)-1H-pyrrolo[3,2-b]pyridin-1-yl}-2,4-difluorophenyl)propane-1-sulfonamide
C28 H31 F2 N7 O3 S
VAUBUHYXHFOSFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.265 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.059α = 90
b = 104.244β = 90
c = 109.904γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2020-08-26
    Changes: Database references
  • Version 1.2: 2020-10-28
    Changes: Database references
  • Version 2.0: 2021-03-31
    Changes: Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description