3VNT

Crystal Structure of the Kinase domain of Human VEGFR2 with a [1,3]thiazolo[5,4-b]pyridine derivative

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Design and synthesis of novel DFG-out RAF/vascular endothelial growth factor receptor 2 (VEGFR2) inhibitors. 1. Exploration of [5,6]-fused bicyclic scaffolds

Okaniwa, M., Hirose, M., Imada, T., Ohashi, T., Hayashi, Y., Miyazaki, T., Arita, T., Yabuki, M., Kakoi, K., Kato, J., Takagi, T., Kawamoto, T., Yao, S., Sumita, A., Tsutsumi, S., Tottori, T., Oki, H., Sang, B.C., Yano, J., Aertgeerts, K., Yoshida, S., Ishikawa, T.

(2012) J.Med.Chem. 55: 3452-3478

  • DOI: 10.1021/jm300126x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • To develop RAF/VEGFR2 inhibitors that bind to the inactive DFG-out conformation, we conducted structure-based drug design using the X-ray cocrystal structures of BRAF, starting from an imidazo[1,2-b]pyridazine derivative. We designed various [5,6]-fu ...

    To develop RAF/VEGFR2 inhibitors that bind to the inactive DFG-out conformation, we conducted structure-based drug design using the X-ray cocrystal structures of BRAF, starting from an imidazo[1,2-b]pyridazine derivative. We designed various [5,6]-fused bicyclic scaffolds (ring A, 1-6) possessing an anilide group that forms two hydrogen bond interactions with Cys532. Stabilizing the planarity of this anilide and the nitrogen atom on the six-membered ring of the scaffold was critical for enhancing BRAF inhibition. The selected [1,3]thiazolo[5,4-b]pyridine derivative 6d showed potent inhibitory activity in both BRAF and VEGFR2. Solid dispersion formulation of 6d (6d-SD) maximized its oral absorption in rats and showed significant suppression of ERK1/2 phosphorylation in an A375 melanoma xenograft model in rats by single administration. Tumor regression (T/C = -7.0%) in twice-daily repetitive studies at a dose of 50 mg/kg in rats confirmed that 6d is a promising RAF/VEGFR2 inhibitor showing potent anticancer activity.

    Organizational Affiliation: 

    Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan. masanori.okaniwa@takeda.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vascular endothelial growth factor receptor 2
A
318Homo sapiensMutation(s): 0 
Gene Names: KDR (FLK1, VEGFR2)
EC: 2.7.10.1
Find proteins for P35968 (Homo sapiens)
Go to Gene View: KDR
Go to UniProtKB:  P35968
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO
Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
0JA
Query on 0JA
Download SDF File 
Download CCD File 
A
2-chloro-3-(1-cyanocyclopropyl)-N-[5-({2-[(cyclopropylcarbonyl)amino][1,3]thiazolo[5,4-b]pyridin-5-yl}oxy)-2-fluorophenyl]benzamide
C27 H19 Cl F N5 O3 S
MDPMAXSABUPRJI-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0JAIC50: 2.2 nM BINDINGMOAD
0JAIC50: 2.2 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.151 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 135.615α = 90.00
b = 56.618β = 94.88
c = 51.819γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2012-01-17 
  • Released Date: 2012-04-11 
  • Deposition Author(s): Oki, H.

Revision History 

  • Version 1.0: 2012-04-11
    Type: Initial release
  • Version 1.1: 2013-08-07
    Type: Database references