Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.72 kDa 
• Atom Count: 2,673 
• Modelled Residue Count: 292 
• Deposited Residue Count: 314 
• Unique protein chains: 1

 2P2H

Crystal structure of the VEGFR2 kinase domain in complex with a pyridinyl-triazine inhibitor

• PDB DOI: 10.2210/pdb2P2H/pdb

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


• Deposited: 2007-03-07 Released: 2007-03-20 
• Deposition Author(s): Whittington, D.A., Kim, J.L., Long, A.M., Rose, P., Gu, Y., Zhao, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.229 
• R-Value Work: 0.205 

Literature

Evolution of a Highly Selective and Potent 2-(Pyridin-2-yl)-1,3,5-triazine Tie-2 Kinase Inhibitor

Hodous, B.L., Geuns-Meyer, S.D., Hughes, P.E., Albrecht, B.K., Bellon, S., Bready, J., Caenepeel, S., Cee, V.J., Chaffee, S.C., Coxon, A., Emery, M., Fretland, J., Gallant, P., Gu, Y., Hoffman, D., Johnson, R.E., Kendall, R., Kim, J.L., Long, A.M., Morrison, M., Olivieri, P.R., Patel, V.F., Polverino, A., Rose, P., Tempest, P., Wang, L., Whittington, D.A., Zhao, H.

(2007) J Med Chem 50: 611-626

• PubMed: 17253678 
• DOI: 10.1021/jm061107l
• Primary Citation of Related Structures:  
  2P2H, 2P2I, 2P4I


• PubMed Abstract: 
  

Inhibition of angiogenesis is a promising and clinically validated approach for limiting tumor growth and survival. The receptor tyrosine kinase Tie-2 is expressed almost exclusively in the vascular endothelium and is required for developmental angiogenesis and vessel maturation. However, the significance of Tie-2 signaling in tumor angiogenesis is not well understood. In order to evaluate the therapeutic utility of inhibiting Tie-2 signaling, we developed a series of potent and orally bioavailable small molecule Tie-2 kinase inhibitors with selectivity over other kinases, especially those that are believed to be important for tumor angiogenesis. Our earlier work provided pyridinyl pyrimidine 6 as a potent, nonselective Tie-2 inhibitor that was designed on the basis of X-ray cocrystal structures of KDR inhibitors 34 (triazine) and 35 (nicotinamide). Lead optimization resulted in pyridinyl triazine 63, which exhibited >30-fold selectivity over a panel of kinases, good oral exposure, and in vivo inhibition of Tie-2 phosphorylation.

---

Organizational Affiliation: 

Department of Medicinal Chemistry, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139-1581, 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
994	B [auth A]	4-(2-anilinopyridin-3-yl)-N-(3,4,5-trimethoxyphenyl)-1,3,5-triazin-2-amine C23 H22 N6 O3 YRSYWYSGZPRSOP-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
994	Binding MOAD:  2P2H	IC50: 68 (nM) from 1 assay(s)
	BindingDB:  2P2H	IC50: 68 (nM) from 1 assay(s)
	PDBBind:  2P2H	IC50: 68 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.229 
• R-Value Work: 0.205 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.595	α = 90
b = 136.915	β = 90
c = 58.725	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-20 
Deposition Author(s): Whittington, D.A., Kim, J.L., Long, A.M., Rose, P., Gu, Y., Zhao, H.

Revision History  

• Version 1.0: 2007-03-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-08-16
  Changes: Refinement description, Source and taxonomy
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations