3CP9

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

• PDB DOI: https://doi.org/10.2210/pdb3CP9/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2008-03-31 Released: 2008-06-17 
• Deposition Author(s): Whittington, D.A., Long, A.M., Rose, P., Gu, Y., Zhao, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.263 
• R-Value Work: 0.211 

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

• PubMed: 18447379 
• 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. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 73.36 kDa 
• Atom Count: 4,669 
• Modelled Residue Count: 557 
• Deposited Residue Count: 628 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor receptor 2	A, B	314	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C19	C [auth A], D [auth B]	3-(2-aminoquinazolin-6-yl)-1-(3,3-dimethylindolin-6-yl)-4-methylpyridin-2(1H)-one C24 H23 N5 O LHLGUOHREUTYTO-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A, B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
C19	BindingDB:  3CP9	IC50: 48 (nM) from 1 assay(s)
	PDBBind:  3CP9	IC50: 48 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.263 
• R-Value Work: 0.211 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.57	α = 90
b = 67.17	β = 93.076
c = 89.102	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-17 
Deposition Author(s): Whittington, D.A., Long, A.M., Rose, P., Gu, Y., Zhao, H.

Revision History  

• 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: 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
• Version 1.6: 2024-10-30
  Changes: Structure summary