4E4X

Crystal Structure of B-Raf Kinase Domain in Complex with a Dihydropyrido[2,3-d]pyrimidinone-based Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.273 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The discovery of potent and selective pyridopyrimidin-7-one based inhibitors of B-Raf(V600E) kinase.

Ren, L.Ahrendt, K.A.Grina, J.Laird, E.R.Buckmelter, A.J.Hansen, J.D.Newhouse, B.Moreno, D.Wenglowsky, S.Dinkel, V.Gloor, S.L.Hastings, G.Rana, S.Rasor, K.Risom, T.Sturgis, H.L.Voegtli, W.C.Mathieu, S.

(2012) Bioorg.Med.Chem.Lett. 22: 3387-3391

  • DOI: 10.1016/j.bmcl.2012.04.015

  • PubMed Abstract: 
  • Herein we describe the discovery of a novel series of ATP competitive B-Raf inhibitors via structure based drug design (SBDD). These pyridopyrimidin-7-one based inhibitors exhibit both excellent cellular potency and striking B-Raf selectivity. Optimi ...

    Herein we describe the discovery of a novel series of ATP competitive B-Raf inhibitors via structure based drug design (SBDD). These pyridopyrimidin-7-one based inhibitors exhibit both excellent cellular potency and striking B-Raf selectivity. Optimization led to the identification of compound 17, a potent, selective and orally available agent with excellent pharmacokinetic properties and robust tumor growth inhibition in xenograft studies.


    Organizational Affiliation

    Array BioPharma, Inc., 3200 Walnut Street, Boulder, CO 80301, United States. li.ren@arraybiopharma.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase B-raf
A, B
307Homo 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
T1Q
Query on T1Q

Download SDF File 
Download CCD File 
A, B
N-(2,4-difluoro-3-{2-[(3-hydroxypropyl)amino]-8-methyl-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-6-yl}phenyl)propane-1-sulfonamide
C20 H23 F2 N5 O4 S
HCWAUGCXCGOSNN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
T1QIC50: 7 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.273 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 109.000α = 90.00
b = 109.000β = 90.00
c = 155.210γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
ADSCdata collection
CNSrefinement
MOSFLMdata reduction
CNXrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-09
    Type: Initial release
  • Version 1.1: 2012-05-23
    Type: Database references