6NSQ

Crystal structure of BRAF kinase domain bound to the inhibitor 2l


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Rigidification Dramatically Improves Inhibitor Selectivity for RAF Kinases.

Assadieskandar, A.Yu, C.Maisonneuve, P.Kurinov, I.Sicheri, F.Zhang, C.

(2019) Acs Med.Chem.Lett. 10: 1074-1080

  • DOI: 10.1021/acsmedchemlett.9b00194

  • PubMed Abstract: 
  • One effective means to achieve inhibitor specificity for RAF kinases, an important family of cancer drug targets, has been to target the monomeric inactive state conformation of the kinase domain, which, unlike most other kinases, can accommodate sul ...

    One effective means to achieve inhibitor specificity for RAF kinases, an important family of cancer drug targets, has been to target the monomeric inactive state conformation of the kinase domain, which, unlike most other kinases, can accommodate sulfonamide-containing drugs such as vemurafenib and dabrafenib because of the presence of a unique pocket specific to inactive RAF kinases. We previously reported an alternate strategy whereby rigidification of a nonselective pyrazolo[3,4- d ]pyrimidine-based inhibitor through ring closure afforded moderate but appreciable increases in selectivity for RAF kinases. Here, we show that a further application of the rigidification strategy to a different pyrazolopyrimidine-based scaffold dramatically improved selectivity for RAF kinases. Crystal structure analysis confirmed our inhibitor design hypothesis revealing that 2l engages an active-like state conformation of BRAF normally associated with poorly discriminating inhibitors. When screened against a panel of distinct cancer cell lines, the optimized inhibitor 2l primarily inhibited the proliferation of the expected BRAF V600E -harboring cell lines consistent with its kinome selectivity profile. These results suggest that rigidification could be a general and powerful strategy for enhancing inhibitor selectivity against protein kinases, which may open up therapeutic opportunities not afforded by other approaches.


    Organizational Affiliation

    Loker Hydrocarbon Research Institute & Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States.,Departments of Molecular Genetics and Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5 Canada.,Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, Illinois 60439, United States.,USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase B-raf
B, A
284Homo sapiensMutation(s): 16 
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KZP
Query on KZP

Download SDF File 
Download CCD File 
A, B
5-[(4-amino-1-ethyl-1H-pyrazolo[3,4-d]pyrimidin-3-yl)ethynyl]-N-(4-chlorophenyl)-6-methylisoquinolin-1-amine
C25 H20 Cl N7
AZFFXPMHTGBCGM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.235 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.543α = 90.00
b = 89.393β = 90.00
c = 112.982γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-07-31
    Type: Data collection, Database references