3DTW

Crystal structure of the VEGFR2 kinase domain in complex with a benzisoxazole inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.279 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.200 (DCC) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A96Click on this verticalbar to view details

This is version 1.5 of the entry. See complete history


Literature

Discovery of amido-benzisoxazoles as potent c-Kit inhibitors.

Kunz, R.K.Rumfelt, S.Chen, N.Zhang, D.Tasker, A.S.Burli, R.Hungate, R.Yu, V.Nguyen, Y.Whittington, D.A.Meagher, K.L.Plant, M.Tudor, Y.Schrag, M.Xu, Y.Ng, G.Y.Hu, E.

(2008) Bioorg Med Chem Lett 18: 5115-5117

  • DOI: https://doi.org/10.1016/j.bmcl.2008.07.111
  • Primary Citation of Related Structures:  
    3DTW

  • PubMed Abstract: 

    Deregulation of the receptor tyrosine kinase c-Kit is associated with an increasing number of human diseases, including certain cancers and mast cell diseases. Interference of c-Kit signaling with multi-kinase inhibitors has been shown clinically to successfully treat gastrointestinal stromal tumors and mastocytosis. Targeted therapy of c-Kit activity may provide therapeutic advantages against off-target effects for non-oncology applications. A new structural class of c-Kit inhibitors is described, including in vitro c-Kit potency, kinase selectivity, and the observed binding mode.


  • Organizational Affiliation

    Department of Medicinal Chemistry, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA. kunz@amgen.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vascular endothelial growth factor receptor 2
A, B
314Homo sapiensMutation(s): 3 
Gene Names: KDRFLK1
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P35968 (Homo sapiens)
Explore P35968 
Go to UniProtKB:  P35968
PHAROS:  P35968
GTEx:  ENSG00000128052 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35968
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A96
Query on A96

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
6-chloro-N-pyrimidin-5-yl-3-{[3-(trifluoromethyl)phenyl]amino}-1,2-benzisoxazole-7-carboxamide
C19 H11 Cl F3 N5 O2
FEGRQUWSKADGSP-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A, B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Binding Affinity Annotations 
IDSourceBinding Affinity
A96 BindingDB:  3DTW IC50: 353 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.279 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.200 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.244α = 90
b = 68.355β = 92.16
c = 88.485γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A96Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-08-23
    Changes: Source and taxonomy
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-02-21
    Changes: Data collection
  • Version 1.5: 2024-11-13
    Changes: Structure summary