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: 3.60 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.275 

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
  • Primary Citation of Related Structures:  
    4E4X

  • 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. 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-rafA, B307Homo sapiensMutation(s): 0 
Gene Names: BRAFBRAF1RAFB1
EC: 2.7.11.1
Find proteins for P15056 (Homo sapiens)
Explore P15056 
Go to UniProtKB:  P15056
NIH Common Fund Data Resources
PHAROS:  P15056
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T1Q
Query on T1Q

Download Ideal Coordinates CCD File 
C [auth A], D [auth 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: 3.60 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.275 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109α = 90
b = 109β = 90
c = 155.21γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
CNXrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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