5FD2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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: 10.1016/j.bmc.2016.03.055

  • 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 s ...

    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 Medicinal Chemistry, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, USA. Electronic address: lliu@amgen.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase B-raf
A, B
300Homo 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
5XJ
Query on 5XJ

Download SDF File 
Download CCD File 
A, B
6-[2-[[3-(dimethylsulfamoylamino)-2,6-bis(fluoranyl)phenyl]amino]pyridin-3-yl]-7~{H}-purine
C18 H16 F2 N8 O2 S
DFMZBEXLPWVTSV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.213 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 73.790α = 90.00
b = 80.088β = 90.00
c = 245.253γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data scaling
EPMRphasing
Cootmodel building
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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