4EHE | pdb_00004ehe

B-Raf Kinase Domain in Complex with an Aminothienopyrimidine-based Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.296 (Depositor) 
  • R-Value Work: 
    0.225 (Depositor) 
  • R-Value Observed: 
    0.228 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4EHE

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Potent and selective aminopyrimidine-based B-raf inhibitors with favorable physicochemical and pharmacokinetic properties.

Mathieu, S.Gradl, S.N.Ren, L.Wen, Z.Aliagas, I.Gunzner-Toste, J.Lee, W.Pulk, R.Zhao, G.Alicke, B.Boggs, J.W.Buckmelter, A.J.Choo, E.F.Dinkel, V.Gloor, S.L.Gould, S.E.Hansen, J.D.Hastings, G.Hatzivassiliou, G.Laird, E.R.Moreno, D.Ran, Y.Voegtli, W.C.Wenglowsky, S.Grina, J.Rudolph, J.

(2012) J Med Chem 55: 2869-2881

  • DOI: https://doi.org/10.1021/jm300016v
  • Primary Citation Related Structures: 
    4EHE, 4EHG

  • PubMed Abstract: 

    Recent clinical data provided proof-of-concept for selective B-Raf inhibitors in treatment of B-Raf(V600E) mutant melanoma. Pyrazolopyridine-type B-Raf inhibitors previously described by the authors are potent and selective but exhibit low solubility requiring the use of amorphous dispersion-based formulation for achieving efficacious drug exposures. Through structure-based design, we discovered a new class of highly potent aminopyrimidine-based B-Raf inhibitors with improved solubility and pharmacokinetic profiles. The hinge binding moiety possesses a basic center imparting high solubility at gastric pH, addressing the dissolution limitation observed with our previous series. In our search for an optimal linker-hinge binding moiety system, amide-linked thieno[3,2-d]pyrimidine analogues 32 and 35 (G945), molecules with desirable physicochemical properties, emerged as lead compounds with strong efficacy in a B-Raf(V600E) mutant mouse xenograft model. Synthesis, SAR, lead selection, and evaluation of key compounds in animal studies will be described.


  • Organizational Affiliation
    • Genentech, Inc., 1 DNA Way, South San Francisco, California 94080-4990, United States.

Macromolecule Content 

  • Total Structure Weight: 71.29 kDa 
  • Atom Count: 4,392 
  • Modeled Residue Count: 542 
  • Deposited Residue Count: 614 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-raf
A, B
307Homo 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
GTEx:  ENSG00000157764 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15056
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RI8

Query on RI8



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
4-amino-N-{2,6-difluoro-3-[(propylsulfonyl)amino]phenyl}thieno[3,2-d]pyrimidine-7-carboxamide
C16 H15 F2 N5 O3 S2
WWRQXSNKYPVJOU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.296 (Depositor) 
  • R-Value Work:  0.225 (Depositor) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.196α = 90
b = 108.196β = 90
c = 153.103γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations