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 
  • R-Value Observed: 0.216 

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
  • Primary Citation of Related Structures:  
    5FD2

  • 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) ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-rafA, B300Homo sapiensMutation(s): 0 
Gene Names: BRAFBRAF1RAFB1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P15056 (Homo sapiens)
Explore P15056 
Go to UniProtKB:  P15056
PHAROS:  P15056
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5XJ
Query on 5XJ

Download Ideal Coordinates CCD File 
C [auth A], D [auth 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 
  • 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
REFMACrefinement
HKL-2000data scaling
EPMRphasing
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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