3CPC | pdb_00003cpc

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.272 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.216 (DCC) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history. 

Literature

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 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

Macromolecule Content 

  • Total Structure Weight: 73.36 kDa 
  • Atom Count: 4,580 
  • Modeled Residue Count: 546 
  • Deposited Residue Count: 628 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Vascular endothelial growth factor receptor 2
A, B
314Homo sapiensMutation(s): 3 
Gene Names: KDR, FLK1
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C52

Query on C52


Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]		3-(2-aminoquinazolin-6-yl)-4-methyl-1-[3-(trifluoromethyl)phenyl]pyridin-2(1H)-one
C21 H15 F3 N4 O
HXUZQEYFKAZBPX-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
C52 BindingDB:  3CPC IC50: 5000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.272 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.216 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.361α = 90
b = 66.865β = 93.352
c = 89.858γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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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: Advisory, Refinement description, 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
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-02-21
    Changes: Data collection
  • Version 1.6: 2024-11-06
    Changes: Structure summary