5JRQ

BRAFV600E Kinase Domain In Complex with Chemically Linked Vemurafenib Inhibitor VEM-6-VEM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.287 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Chemically Linked Vemurafenib Inhibitors Promote an Inactive BRAF(V600E) Conformation.

Grasso, M.Estrada, M.A.Ventocilla, C.Samanta, M.Maksimoska, J.Villanueva, J.Winkler, J.D.Marmorstein, R.

(2016) Acs Chem.Biol. 11: 2876-2888

  • DOI: 10.1021/acschembio.6b00529
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The BRAF kinase, within the mitogen activated protein kinase (MAPK) signaling pathway, harbors activating mutations in about half of melanomas and to a significant extent in many other cancers. A single valine to glutamic acid substitution at residue ...

    The BRAF kinase, within the mitogen activated protein kinase (MAPK) signaling pathway, harbors activating mutations in about half of melanomas and to a significant extent in many other cancers. A single valine to glutamic acid substitution at residue 600 (BRAFV600E) accounts for about 90% of these activating mutations. While BRAFV600E-selective small molecule inhibitors, such as debrafenib and vemurafenib, have shown therapeutic benefit, almost all patients develop resistance. Resistance often arises through reactivation of the MAPK pathway, typically through mutation of upstream RAS, downstream MEK, or splicing variants. RAF kinases signal as homo- and heterodimers, and another complication associated with small molecule BRAFV600E inhibition is drug-induced allosteric activation of a wild-type RAF subunit (BRAF or CRAF) of the kinase dimer, a process called "transactivation" or "paradoxical activation." Here, we used BRAFV600E and vemurafenib as a model system to develop chemically linked kinase inhibitors to lock RAF dimers in an inactive conformation that cannot undergo transactivation. This structure-based design effort resulted in the development of Vem-BisAmide-2, a compound containing two vemurafenib molecules connected by a bis amide linker. We show that Vem-BisAmide-2 has comparable inhibitory potency as vemurafenib to BRAFV600E both in vitro and in cells but promotes an inactive dimeric BRAFV600E conformation unable to undergo transactivation. The crystal structure of a BRAFV600E/Vem-BisAmide-2 complex and associated biochemical studies reveal the molecular basis for how Vem-BisAmide-2 mediates selectivity for an inactive over an active dimeric BRAFV600E conformation. These studies have implications for targeting BRAFV600E/RAF heterodimers and other kinase dimers for therapy.


    Organizational Affiliation

    Department of Biochemistry and Biophysics and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania , 421 Curie Blvd., Philadelphia, Pennsylvania 19104, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase B-raf
A, B
280Homo sapiensMutation(s): 17 
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6N9
Query on 6N9

Download SDF File 
Download CCD File 
A, B
(3-{[dihydroxy(propyl)-lambda~4~-sulfanyl]amino}-2,6-difluorophenyl)[5-(4-methoxyphenyl)-1H-pyrrolo[2,3-b]pyridin-3-yl]methanone
C24 H23 F2 N3 O4 S
XAALTFVMAMULHB-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
TMA
Query on TMA

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Download CCD File 
A, B
TETRAMETHYLAMMONIUM ION
C4 H12 N
QEMXHQIAXOOASZ-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A, B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.287 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.836α = 90.00
b = 67.753β = 90.32
c = 67.881γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
Cootmodel building
HKL-3000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA114046

Revision History 

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-09-21
    Type: Database references
  • Version 1.2: 2016-11-02
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Derived calculations
  • Version 1.4: 2019-12-04
    Type: Author supporting evidence