6CAD

Crystal structure of RAF kinase domain bound to the inhibitor 2a

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.256 

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Literature

Effects of rigidity on the selectivity of protein kinase inhibitors.

Assadieskandar, A., Yu, C., Maisonneuve, P., Liu, X., Chen, Y.C., Prakash, G.K.S., Kurinov, I., Sicheri, F., Zhang, C.

(2018) Eur J Med Chem 146: 519-528

  • DOI: 10.1016/j.ejmech.2018.01.053
  • Primary Citation of Related Structures:  
    6CAD

  • PubMed Abstract: 

    • Established strategies for discovering selective kinase inhibitors are target-centric as they often target certain structural or reactive features in the target kinase. In the absence of such prominent features, there is a lack of general methods for discovering selective inhibitors ...

    Established strategies for discovering selective kinase inhibitors are target-centric as they often target certain structural or reactive features in the target kinase. In the absence of such prominent features, there is a lack of general methods for discovering selective inhibitors. Here we describe a new strategy that exploits conformational flexibility of kinases for achieving selective kinase inhibition. Through ring closure, we designed and synthesized a panel of isoquinoline-containing compounds as rigidified analogs of an amidophenyl-containing parent compound. These analogs potently inhibit kinases including Abl and BRAF but have diminished inhibition against some other kinases compared to the parent compound. Sequence analysis reveals that many of the kinases that are potently inhibited by the isoquonoline-containing compounds contain a long insertion within their catalytic domains. A crystal structure of one rigid compound bound to BRAF confirmed its binding mode. Our findings highlight the potential of a novel strategy of rigidification for improving the selectivity of kinase inhibitors.

    Organizational Affiliation: 

    Loker Hydrocarbon Research Institute & Department of Chemistry, University of Southern California, University Park, Los Angeles, CA 90089, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA. Electronic address: zhang.chao@usc.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-rafA, B284Homo sapiensMutation(s): 16 
Gene Names: BRAF, BRAF1, RAFB1
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15056
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EU4
Query on EU4
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		1-(propan-2-yl)-3-({3-[3-(trifluoromethyl)phenyl]isoquinolin-8-yl}ethynyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
C26 H19 F3 N6
OFBWCZMTFNTSHE-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EU4 BindingDB:  6CAD IC50: min: 14, max: 1.00e+4 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.256 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.493α = 90
b = 114.548β = 90
c = 55.599γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-21
    Type: Initial release