3DTW

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

• PDB DOI: https://doi.org/10.2210/pdb3DTW/pdb

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


• Deposited: 2008-07-16 Released: 2008-09-09 
• Deposition Author(s): Whittington, D.A., Long, A.M., Rose, P., Gu, Y., Zhao, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.279 
• R-Value Work: 0.215 

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

• PubMed: 18723346 
• 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.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Amgen Inc., One Amgen Center Drive, 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: 73.44 kDa 
• Atom Count: 4,574 
• 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
A96	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
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
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 
• R-Value Work: 0.215 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.244	α = 90
b = 68.355	β = 92.16
c = 88.485	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: 2008-09-09 
Deposition Author(s): Whittington, D.A., Long, A.M., Rose, P., Gu, Y., Zhao, H.

Revision History  

• 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