Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.78 kDa 
• Atom Count: 2,544 
• Modelled Residue Count: 294 
• Deposited Residue Count: 314 
• Unique protein chains: 1

 2RL5

Crystal structure of the VEGFR2 kinase domain in complex with a 2,3-dihydro-1,4-benzoxazine inhibitor

• PDB DOI:  https://doi.org/10.2210/pdb2RL5/pdb

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


• Deposited: 2007-10-18 Released: 2008-04-08 
• Deposition Author(s): Whittington, D.A., Long, A.M., Rose, P., Zhao, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.233 
• R-Value Work: 0.199 

Literature

Novel 2,3-dihydro-1,4-benzoxazines as potent and orally bioavailable inhibitors of tumor-driven angiogenesis.

La, D.S., Belzile, J., Bready, J.V., Coxon, A., Demelfi, T., Doerr, N., Estrada, J., Flynn, J.C., Flynn, S.R., Graceffa, R.F., Harriman, S.P., Larrow, J.F., Long, A.M., Martin, M.W., Morrison, M.J., Patel, V.F., Roveto, P.M., Wang, L., Weiss, M.M., Whittington, D.A., Teffera, Y., Zhao, Z., Polverino, A.J., Harmange, J.C.

(2008) J Med Chem 51: 1695-1705

• PubMed: 18311900 
• DOI: https://doi.org/10.1021/jm701129j
• Primary Citation of Related Structures:  
  2RL5


• PubMed Abstract: 
  

Angiogenesis is vital for solid tumor growth, and its prevention is a proven strategy for the treatment of disease states such as cancer. The vascular endothelial growth factor (VEGF) pathway provides several opportunities by which small molecules can act as inhibitors of endothelial proliferation and migration. Critical to these processes is signaling through VEGFR-2 or the kinase insert domain receptor (KDR) upon stimulation by its ligand VEGF. Herein, we report the discovery of 2,3-dihydro-1,4-benzoxazines as inhibitors of intrinsic KDR activity (IC 50 < 0.1 microM) and human umbilical vein endothelial cell (HUVEC) proliferation with IC 50 < 0.1 microM. More specifically, compound 16 was identified as a potent (KDR: < 1 nM and HUVEC: 4 nM) and selective inhibitor that exhibited efficacy in angiogenic in vivo models. In addition, this series of molecules is typically well-absorbed orally, further demonstrating the 2,3-dihydro-1,4-benzoxazine moiety as a promising platform for generating kinase-based antiangiogenic therapeutic agents.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Amgen Inc., One Kendall Square, Cambridge, MA 02139, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor receptor 2	A	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2RL	B [auth A]	N-(4-CHLOROPHENYL)-7-[(6,7-DIMETHOXYQUINOLIN-4-YL)OXY]-2,3-DIHYDRO-1,4-BENZOXAZINE-4-CARBOXAMIDE C26 H22 Cl N3 O5 RNHWXYKRVZUXGO-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
2RL	PDBBind:  2RL5	IC50: 4 (nM) from 1 assay(s)
	BindingDB:  2RL5	IC50: min: 0.5, max: 0.5 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.233 
• R-Value Work: 0.199 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.76	α = 90
b = 139.774	β = 90
c = 57.55	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: 2008-04-08 
Deposition Author(s): Whittington, D.A., Long, A.M., Rose, P., Zhao, H.

Revision History  

• Version 1.0: 2008-04-08
  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: 2019-11-13
  Changes: Structure summary
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations