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

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.219 

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This is version 1.5 of the entry. See complete history


Discovery of Aryl Aminoquinazoline Pyridones as Potent, Selective, and Orally Efficacious Inhibitors of Receptor Tyrosine Kinase c-Kit.

Hu, E.Tasker, A.White, R.D.Kunz, R.K.Human, J.Chen, N.Burli, R.Hungate, R.Novak, P.Itano, A.Zhang, X.Yu, V.Nguyen, Y.Tudor, Y.Plant, M.Flynn, S.Xu, Y.Meagher, K.L.Whittington, D.A.Ng, G.Y.

(2008) J Med Chem 51: 3065-3068

  • DOI: https://doi.org/10.1021/jm800188g
  • Primary Citation of Related Structures:  
    3CP9, 3CPB, 3CPC

  • PubMed Abstract: 

    Inhibition of c-Kit has the potential to treat mast cell associated fibrotic diseases. We report the discovery of several aminoquinazoline pyridones that are potent inhibitors of c-Kit with greater than 200-fold selectivity against KDR, p38, Lck, and Src. In vivo efficacy of pyridone 16 by dose-dependent inhibition of histamine release was demonstrated in a rodent pharmacodynamic model of mast cell activation.

  • Organizational Affiliation

    Department of Medicinal Chemistry, Amgen Inc, Thousand Oaks, CA 91320-1799, USA. ehu@amgen.com

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
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on C92

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C21 H26 N4 O2
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PTR
A, B
Binding Affinity Annotations 
IDSourceBinding Affinity
C92 BindingDB:  3CPB IC50: 2.50e+4 (nM) from 1 assay(s)
PDBBind:  3CPB IC50: 2.50e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.919α = 90
b = 67.552β = 92.524
c = 88.73γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-07-26
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2018-06-13
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-02-21
    Changes: Data collection