Crystal Structure of Human Kinase Domain of B-raf with a DFG-out Inhibitor

Experimental Data Snapshot

  • Resolution: 2.95 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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Design and synthesis of novel DFG-out RAF/vascular endothelial growth factor receptor 2 (VEGFR2) inhibitors: 3. Evaluation of 5-amino-linked thiazolo[5,4-d]pyrimidine and thiazolo[5,4-b]pyridine derivatives.

Hirose, M.Okaniwa, M.Miyazaki, T.Imada, T.Ohashi, T.Tanaka, Y.Arita, T.Yabuki, M.Kawamoto, T.Tsutsumi, S.Sumita, A.Takagi, T.Sang, B.C.Yano, J.Aertgeerts, K.Yoshida, S.Ishikawa, T.

(2012) Bioorg Med Chem 20: 5600-5615

  • DOI: https://doi.org/10.1016/j.bmc.2012.07.032
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Our aim was to discover RAF/vascular endothelial growth factor receptor 2 (VEGFR2) inhibitors that possess strong activity and sufficient oral absorption, and thus, we selected a 5-amino-linked thiazolo[5,4-d]pyrimidine derivative as the lead compound because of its potential kinase inhibitory activities and its desired solubility. The novel tertiary 1-cyano-1-methylethoxy substituent was designed to occupy the hydrophobic region of 'back pocket' of BRAF on the basis of the X-ray co-crystal structure data of BRAF. In addition, we found that N-methylation of the amine linker could control the twisted molecular conformation leading to improved solubility. These approaches produced N-methyl thiazolo[5,4-b]pyridine-5-amine derivative 5. To maximize the in vivo efficacy, we attempted salt formation of 5. Our result indicated that the besylate monohydrate salt form (5c) showed significant improvement of both solubility and oral absorption. Owing to the improved physicochemical properties, compound 5c demonstrated regressive antitumor efficacy in a HT-29 xenograft model.

  • Organizational Affiliation

    Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited: 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan. masaaki.hirose@takeda.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-raf
A, B
284Homo sapiensMutation(s): 0 
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0T2

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C28 H24 Cl F N6 O3 S
Binding Affinity Annotations 
IDSourceBinding Affinity
0T2 BindingDB:  4FC0 IC50: 69 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.95 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.968α = 90
b = 109.968β = 90
c = 145.973γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-08
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations