3VHK

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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

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

  • DOI: 10.1021/ml3000403
  • Primary Citation of Related Structures:  

  • 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 ...

    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.

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vascular endothelial growth factor receptor 2
A
368Homo sapiensMutation(s): 0 
Gene Names: KDR (FLK1, VEGFR2)
EC: 2.7.10.1
Find proteins for P35968 (Homo sapiens)
Go to Gene View: KDR
Go to UniProtKB:  P35968
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO
Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
BPK
Query on BPK
Download SDF File 
Download CCD File 
A
{3-[(5-methyl-2-phenyl-1,3-oxazol-4-yl)methoxy]phenyl}methanol
C18 H17 N O3
UPVJJOGZAKVERR-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BPKIC50: 50000 - 100000 nM (99) BINDINGDB
BPKKi: 25000 nM (99) BINDINGDB
BPKKi: 25000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 135.719α = 90.00
b = 56.354β = 95.61
c = 51.875γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
d*TREKdata reduction
CrystalCleardata reduction
MOLREPphasing
d*TREKdata scaling
CrystalCleardata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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