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: 42.16 kDa 
• Atom Count: 2463 
• Modelled Residue Count: 297 
• Deposited Residue Count: 368 
• Unique protein chains: 1

3VHK

Crystal structure of the VEGFR2 kinase domain in complex with a back pocket binder

• PDB DOI: 10.2210/pdb3VHK/pdb

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


• Deposited: 2011-08-25 Released: 2012-09-05 
• Deposition Author(s): Iwata, H., Oki, H., Okada, K., Takagi, T., Tawada, M., Miyazaki, Y., Imamura, S., Hori, A., Hixon, M.S., Kimura, H., Miki, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.262 
• R-Value Work: 0.207 
• R-Value Observed: 0.210 

Literature

A Back-to-Front Fragment-Based Drug Design Search Strategy Targeting the DFG-Out Pocket of Protein Tyrosine Kinases.

Iwata, H., Oki, H., Okada, K., Takagi, T., Tawada, M., Miyazaki, Y., Imamura, S., Hori, A., Lawson, J.D., Hixon, M.S., Kimura, H., Miki, H.

(2012) ACS Med Chem Lett 3: 342-346

• PubMed: 24900475 
• DOI: 10.1021/ml3000403
• Primary Citation of Related Structures:  
  3VHK, 3VID


• PubMed Abstract: 
  

We present a straightforward process for the discovery of novel back pocket-binding fragment molecules against protein tyrosine kinases. The approach begins by screening against the nonphosphorylated target kinase with subsequent counterscreening of hits against the phosphorylated enzyme. Back pocket-binding fragments are inactive against the phosphorylated kinase. Fragment molecules are of insufficient size to span both regions of the ATP binding pocket; thus, the outcome is binary (back pocket-binding or hinge-binding). Next, fragments with the appropriate binding profile are assayed in combination with a known hinge-binding fragment and subsequently with a known back pocket-binding fragment. Confirmation of back pocket-binding by Yonetani-Theorell plot analysis progresses candidate fragments to crystallization trials. The method is exemplified by a fragment screening campaign against vascular endothelial growth factor receptor 2, and a novel back pocket-binding fragment is presented.

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Organizational Affiliation: 

Discovery Research Laboratories, Oncology Drug Discovery Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd. , 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor receptor 2	A	368	Homo sapiens	Mutation(s): 0  Gene Names: KDR, FLK1, 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BPK	B [auth A]	{3-[(5-methyl-2-phenyl-1,3-oxazol-4-yl)methoxy]phenyl}methanol C18 H17 N O3 UPVJJOGZAKVERR-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BPK	PDBBind:  3VHK	Ki: 2.50e+4 (nM) from 1 assay(s)
	BindingDB:  3VHK	Ki: 2.50e+4 (nM) from 1 assay(s)
		IC50: min: 5.00e+4, max: 1.00e+5 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.262 
• R-Value Work: 0.207 
• R-Value Observed: 0.210 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.719	α = 90
b = 56.354	β = 95.61
c = 51.875	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-08-25 
• Released Date: 2012-09-05 
Deposition Author(s): Iwata, H., Oki, H., Okada, K., Takagi, T., Tawada, M., Miyazaki, Y., Imamura, S., Hori, A., Hixon, M.S., Kimura, H., Miki, H.

Revision History  

• Version 1.0: 2012-09-05
  Type: Initial release
  
• Version 1.1: 2015-04-22
  Changes: Database references