BRAF in complex with N-(4-methyl-3-(1-methyl-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-5-yl)phenyl)-3-(trifluoromethyl)benzamide.

Experimental Data Snapshot

  • Resolution: 2.04 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Design and Discovery ofN-(3-(2-(2-Hydroxyethoxy)-6-morpholinopyridin-4-yl)-4-methylphenyl)-2-(trifluoromethyl)isonicotinamide, a Selective, Efficacious, and Well-Tolerated RAF Inhibitor Targeting RAS Mutant Cancers: The Path to the Clinic.

Ramurthy, S.Taft, B.R.Aversa, R.J.Barsanti, P.A.Burger, M.T.Lou, Y.Nishiguchi, G.A.Rico, A.Setti, L.Smith, A.Subramanian, S.Tamez, V.Tanner, H.Wan, L.Hu, C.Appleton, B.A.Mamo, M.Tandeske, L.Tellew, J.E.Huang, S.Yue, Q.Chaudhary, A.Tian, H.Iyer, R.Hassan, A.Q.Mathews Griner, L.A.La Bonte, L.R.Cooke, V.G.Van Abbema, A.Merritt, H.Gampa, K.Feng, F.Yuan, J.Mishina, Y.Wang, Y.Haling, J.R.Vaziri, S.Hekmat-Nejad, M.Polyakov, V.Zang, R.Sethuraman, V.Amiri, P.Singh, M.Sellers, W.R.Lees, E.Shao, W.Dillon, M.P.Stuart, D.D.

(2020) J Med Chem 63: 2013-2027

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00161
  • Primary Citation of Related Structures:  
    6N0P, 6N0Q

  • PubMed Abstract: 

    Direct pharmacological inhibition of RAS has remained elusive, and efforts to target CRAF have been challenging due to the complex nature of RAF signaling, downstream of activated RAS, and the poor overall kinase selectivity of putative RAF inhibitors. Herein, we describe 15 (LXH254, Aversa, R.; et al. Int. Patent WO2014151616A1, 2014), a selective B/C RAF inhibitor, which was developed by focusing on drug-like properties and selectivity. Our previous tool compound, 3 (RAF709; Nishiguchi, G. A.; et al. J. Med. Chem. 2017 , 60 , 4969), was potent, selective, efficacious, and well tolerated in preclinical models, but the high human intrinsic clearance precluded further development and prompted further investigation of close analogues. A structure-based approach led to a pyridine series with an alcohol side chain that could interact with the DFG loop and significantly improved cell potency. Further mitigation of human intrinsic clearance and time-dependent inhibition led to the discovery of 15 . Due to its excellent properties, it was progressed through toxicology studies and is being tested in phase 1 clinical trials.

  • Organizational Affiliation

    Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, 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
281Homo 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
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on K7S

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C23 H18 F3 N3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.04 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.32α = 90
b = 94.32β = 90
c = 162.34γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
Adxvdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2020-03-18
    Changes: Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references