B-Raf wild-type kinase domain in complex with a purinylpyridinylamino-based inhibitor

Experimental Data Snapshot

  • Resolution: 2.89 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

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Purinylpyridinylamino-based DFG-in/ alpha C-helix-out B-Raf inhibitors: Applying mutant versus wild-type B-Raf selectivity indices for compound profiling.

Liu, L.Lee, M.R.Kim, J.L.Whittington, D.A.Bregman, H.Hua, Z.Lewis, R.T.Martin, M.W.Nishimura, N.Potashman, M.Yang, K.Yi, S.Vaida, K.R.Epstein, L.F.Babij, C.Fernando, M.Carnahan, J.Norman, M.H.

(2016) Bioorg Med Chem 24: 2215-2234

  • DOI: https://doi.org/10.1016/j.bmc.2016.03.055
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    One of the challenges for targeting B-Raf(V600E) with small molecule inhibitors had been achieving adequate selectivity over the wild-type protein B-Raf(WT), as inhibition of the latter has been associated with hyperplasia in normal tissues. Recent studies suggest that B-Raf inhibitors inducing the 'DFG-in/αC-helix-out' conformation (Type IIB) likely will exhibit improved selectivity for B-Raf(V600E). To explore this hypothesis, we transformed Type IIA inhibitor (1) into a series of Type IIB inhibitors (sulfonamides and sulfamides 4-6) and examined the SAR. Three selectivity indices were introduced to facilitate the analyses: the B-Raf(V600E)/B-Raf(WT) biochemical ((b)S), cellular ((c)S) selectivity, and the phospho-ERK activation ((p)A). Our data indicates that α-branched sulfonamides and sulfamides show higher selectivities than the linear derivatives. We rationalized this finding based on analysis of structural information from the literature and provided evidence for a monomeric B-Raf-inhibitor complex previously hypothesized to be responsible for the desired B-Raf(V600E) selectivity.

  • Organizational Affiliation

    Department of Molecular Structure and Characterization, Amgen Inc., 360 Binney St., Cambridge, MA 02142, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-raf
A, B
300Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P15056 (Homo sapiens)
Explore P15056 
Go to UniProtKB:  P15056
PHAROS:  P15056
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 5XJ

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C18 H16 F2 N8 O2 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.89 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.79α = 90
b = 80.088β = 90
c = 245.253γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-04
    Type: Initial release