Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 41.29 kDa 
• Atom Count: 2929 
• Modelled Residue Count: 303 
• Deposited Residue Count: 359 
• Unique protein chains: 1

3VHE

Crystal structure of human VEGFR2 kinase domain with a novel pyrrolopyrimidine inhibitor.

• PDB DOI: 10.2210/pdb3VHE/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-08-24 Released: 2011-11-02 
• Deposition Author(s): Oguro, Y., Miyamoto, N., Okada, K., Takagi, T., Iwata, H., Awazu, Y., Miki, H., Hori, A., Kamiyama, K., Imanura, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.209 
• R-Value Work: 0.186 

Literature

Design, synthesis, and evaluation of 5-methyl-4-phenoxy-5H-pyrrolo[3,2-d]pyrimidine derivatives: novel VEGFR2 kinase inhibitors binding to inactive kinase conformation.

Oguro, Y., Miyamoto, N., Okada, K., Takagi, T., Iwata, H., Awazu, Y., Miki, H., Hori, A., Kamiyama, K., Imamura, S.

(2010) Bioorg Med Chem 18: 7260-7273

• PubMed: 20833055 
• DOI: 10.1016/j.bmc.2010.08.017
• Primary Citation of Related Structures:  
  3VHE


• PubMed Abstract: 
  

We synthesized a series of pyrrolo[3,2-d]pyrimidine derivatives and evaluated their application as type-II inhibitors of vascular endothelial growth factor receptor 2 (VEGFR2) kinase. Incorporation of a diphenylurea moiety at the C4-position of the pyrrolo[3,2-d]pyrimidine core via an oxygen linker resulted in compounds that were potent inhibitors of VEGFR2 kinase. Of these derivatives, compound 20d showed the strongest inhibition of VEGF-stimulated proliferation of human umbilical vein endothelial cells (HUVEC). The co-crystal structure of 20d and VEGFR2 revealed that 20d binds to the inactive form of VEGFR2. Further studies indicated that 20d inhibited VEGFR2 kinase with slow dissociation kinetics and also inhibited PDGFR and Tie-2 kinases. Oral administration of the hydrochloride salt of 20d at 3mg/kg/day showed potent inhibition of tumor growth in a DU145 human prostate cancer cell xenograft nude mouse model.

---

Organizational Affiliation: 

Pharmaceutical Research Division, Takeda Pharmaceutical Co., Ltd, 10, Wadai, Tsukuba, Ibaraki 300-4293, Japan. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor receptor 2	A	359	Homo sapiens	Mutation(s): 0  Gene Names: FLK1, KDR, VEGFR2 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
42Q	B [auth A]	1-{2-fluoro-4-[(5-methyl-5H-pyrrolo[3,2-d]pyrimidin-4-yl)oxy]phenyl}-3-[3-(trifluoromethyl)phenyl]urea C21 H15 F4 N5 O2 TWOLOZGQZKJZKJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
42Q	BindingDB:  3VHE	Ki: min: 0.02, max: 23 (nM) from 4 assay(s)
		Kd: 19 (nM) from 1 assay(s)
		IC50: min: 0.03, max: 46 (nM) from 5 assay(s)
	Binding MOAD:  3VHE	IC50: 6.2 (nM) from 1 assay(s)
	PDBBind:  3VHE	IC50: 6.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.209 
• R-Value Work: 0.186 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.34	α = 90
b = 56.27	β = 95.24
c = 52.07	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
CNX	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-08-24 
• Released Date: 2011-11-02 
Deposition Author(s): Oguro, Y., Miyamoto, N., Okada, K., Takagi, T., Iwata, H., Awazu, Y., Miki, H., Hori, A., Kamiyama, K., Imanura, S.

Revision History  

• Version 1.0: 2011-11-02
  Type: Initial release