4EHG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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: 10.1021/jm300016v
  • Primary Citation of Related Structures:  4EHE

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase B-raf
A, B
307Homo sapiensGene 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
RI9
Query on RI9

Download SDF File 
Download CCD File 
A, B
N-{2,4-difluoro-3-[({6-[(2-hydroxyethyl)amino]pyrimidin-4-yl}carbamoyl)amino]phenyl}propane-1-sulfonamide
C16 H20 F2 N6 O4 S
RFXIGXFNQUUTSZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RI9IC50: 64 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.212 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 100.499α = 90.00
b = 100.499β = 90.00
c = 161.305γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Blu-Icedata collection
REFMACphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-04-02 
  • Released Date: 2013-04-24 
  • Deposition Author(s): Voegtli, W.C.

Revision History 

  • Version 1.0: 2013-04-24
    Type: Initial release