The Complex of wild-type B-RAF with Pyrazolo pyrimidine inhibitor

Experimental Data Snapshot

  • Resolution: 2.79 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

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Non-hinge-binding pyrazolo[1,5-a]pyrimidines as potent B-Raf kinase inhibitors.

Berger, D.M.Torres, N.Dutia, M.Powell, D.Ciszewski, G.Gopalsamy, A.Levin, J.I.Kim, K.H.Xu, W.Wilhelm, J.Hu, Y.Collins, K.Feldberg, L.Kim, S.Frommer, E.Wojciechowicz, D.Mallon, R.

(2009) Bioorg Med Chem Lett 19: 6519-6523

  • DOI: https://doi.org/10.1016/j.bmcl.2009.10.049
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    As part of our research effort to discover B-Raf kinase inhibitors, we prepared a series of C-3 substituted N-(3-(pyrazolo[1,5-a]pyrimidin-7-yl)phenyl)-3-(trifluoromethyl)benzamides. X-ray crystallography studies revealed that one of the more potent inhibitors (10n) bound to B-Raf kinase without forming a hinge-binding hydrogen bond. With basic amine residues appended to C-3 aryl residues, cellular activity and solubility were enhanced over previously described compounds of this class.

  • Organizational Affiliation

    Chemical Sciences, Wyeth Research, Pearl River, NY 10965, USA. bergerd@wyeth.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B-Raf proto-oncogene serine/threonine-protein kinase
A, B
306Homo sapiensMutation(s): 0 
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
Binding Affinity Annotations 
IDSourceBinding Affinity
831 PDBBind:  3II5 IC50: 24 (nM) from 1 assay(s)
BindingDB:  3II5 IC50: 24 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.79 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.219α = 90
b = 110.219β = 90
c = 148.468γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations