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

Experimental Data Snapshot

  • Resolution: 3.05 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

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This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1021/acsmedchemlett.9b00194
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-rafA [auth B],
B [auth A]
284Homo sapiensMutation(s): 16 
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 KZP

Download Ideal Coordinates CCD File 
C [auth B],
D [auth A]
C25 H20 Cl N7
Experimental Data & Validation

Experimental Data

  • Resolution: 3.05 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.543α = 90
b = 89.393β = 90
c = 112.982γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description