5VAL

BRAF in Complex with N-(3-(tert-butyl)phenyl)-4-methyl-3-(6-morpholinopyrimidin-4-yl)benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design and Discovery of N-(2-Methyl-5'-morpholino-6'-((tetrahydro-2H-pyran-4-yl)oxy)-[3,3'-bipyridin]-5-yl)-3-(trifluoromethyl)benzamide (RAF709): A Potent, Selective, and Efficacious RAF Inhibitor Targeting RAS Mutant Cancers.

Nishiguchi, G.A.Rico, A.Tanner, H.Aversa, R.J.Taft, B.R.Subramanian, S.Setti, L.Burger, M.T.Wan, L.Tamez, V.Smith, A.Lou, Y.Barsanti, P.A.Appleton, B.A.Mamo, M.Tandeske, L.Dix, I.Tellew, J.E.Huang, S.Mathews Griner, L.A.Cooke, V.G.Van Abbema, A.Merritt, H.Ma, S.Gampa, K.Feng, F.Yuan, J.Wang, Y.Haling, J.R.Vaziri, S.Hekmat-Nejad, M.Jansen, J.M.Polyakov, V.Zang, R.Sethuraman, V.Amiri, P.Singh, M.Lees, E.Shao, W.Stuart, D.D.Dillon, M.P.Ramurthy, S.

(2017) J. Med. Chem. 60: 4869-4881

  • DOI: 10.1021/acs.jmedchem.6b01862
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • RAS oncogenes have been implicated in >30% of human cancers, all representing high unmet medical need. The exquisite dependency on CRAF kinase in KRAS mutant tumors has been established in genetically engineered mouse models and human tumor cells. To ...

    RAS oncogenes have been implicated in >30% of human cancers, all representing high unmet medical need. The exquisite dependency on CRAF kinase in KRAS mutant tumors has been established in genetically engineered mouse models and human tumor cells. To date, many small molecule approaches are under investigation to target CRAF, yet kinase-selective and cellular potent inhibitors remain challenging to identify. Herein, we describe 14 (RAF709) [ Aversa , Biaryl amide compounds as kinase inhibitors and their preparation . WO 2014151616, 2014 ], a selective B/C RAF inhibitor, which was developed through a hypothesis-driven approach focusing on drug-like properties. A key challenge encountered in the medicinal chemistry campaign was maintaining a balance between good solubility and potent cellular activity (suppression of pMEK and proliferation) in KRAS mutant tumor cell lines. We investigated the small molecule crystal structure of lead molecule 7 and hypothesized that disruption of the crystal packing would improve solubility, which led to a change from N-methylpyridone to a tetrahydropyranyl oxy-pyridine derivative. 14 proved to be soluble, kinase selective, and efficacious in a KRAS mutant xenograft model.


    Organizational Affiliation

    Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 5300 Chiron Way, Emeryville, California 94608, United States.,Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG , Werk Klybeck, Postfach, CH-4002 Basel, Switzerland.,Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.,Oncology, Novartis Institutes for BioMedical Research , 5300 Chiron Way, Emeryville, California 94608, United States.,Genomics Institute of the Novartis Research Foundation , 10675 John Hopkins Drive, San Diego, California 92121, United States.,Oncology, Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase B-raf
A, B
281Homo sapiensMutation(s): 0 
Gene 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
92D
Query on 92D

Download SDF File 
Download CCD File 
A, B
N-(3-tert-butylphenyl)-4-methyl-3-[6-(morpholin-4-yl)pyrimidin-4-yl]benzamide
C26 H30 N4 O2
MVCIEOOXCBYSMB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.181 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 94.121α = 90.00
b = 94.121β = 90.00
c = 163.537γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
BUSTERrefinement
PHASERphasing
Aimlessdata scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-05
    Type: Database references