B-Raf Kinase Domain in Complex with an Aminopyridimine-based Inhibitor

Experimental Data Snapshot

  • Resolution: 3.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

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Potent and selective aminopyrimidine-based B-raf inhibitors with favorable physicochemical and pharmacokinetic properties.

Mathieu, S.Gradl, S.N.Ren, L.Wen, Z.Aliagas, I.Gunzner-Toste, J.Lee, W.Pulk, R.Zhao, G.Alicke, B.Boggs, J.W.Buckmelter, A.J.Choo, E.F.Dinkel, V.Gloor, S.L.Gould, S.E.Hansen, J.D.Hastings, G.Hatzivassiliou, G.Laird, E.R.Moreno, D.Ran, Y.Voegtli, W.C.Wenglowsky, S.Grina, J.Rudolph, J.

(2012) J Med Chem 55: 2869-2881

  • DOI: https://doi.org/10.1021/jm300016v
  • Primary Citation of Related Structures:  
    4EHE, 4EHG

  • PubMed Abstract: 

    Recent clinical data provided proof-of-concept for selective B-Raf inhibitors in treatment of B-Raf(V600E) mutant melanoma. Pyrazolopyridine-type B-Raf inhibitors previously described by the authors are potent and selective but exhibit low solubility requiring the use of amorphous dispersion-based formulation for achieving efficacious drug exposures. Through structure-based design, we discovered a new class of highly potent aminopyrimidine-based B-Raf inhibitors with improved solubility and pharmacokinetic profiles. The hinge binding moiety possesses a basic center imparting high solubility at gastric pH, addressing the dissolution limitation observed with our previous series. In our search for an optimal linker-hinge binding moiety system, amide-linked thieno[3,2-d]pyrimidine analogues 32 and 35 (G945), molecules with desirable physicochemical properties, emerged as lead compounds with strong efficacy in a B-Raf(V600E) mutant mouse xenograft model. Synthesis, SAR, lead selection, and evaluation of key compounds in animal studies will be described.

  • Organizational Affiliation

    Genentech, Inc., 1 DNA Way, South San Francisco, California 94080-4990, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-raf
A, B
307Homo sapiensMutation(s): 1 
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 RI9

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C16 H20 F2 N6 O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
RI9 PDBBind:  4EHG IC50: 64 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.499α = 90
b = 100.499β = 90
c = 161.305γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata 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: 2013-04-24
    Type: Initial release