3VID

Crystal structure of human VEGFR2 kinase domain with Compound A.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.245 

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
356Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4TT
Query on 4TT

Download SDF File 
Download CCD File 
A
4,5,6,11-tetrahydro-1H-pyrazolo[4',3':6,7]cyclohepta[1,2-b]indole
C14 H13 N3
HBWXPQZQCDQNND-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4TTIC50: 620 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.245 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.240α = 90.00
b = 94.620β = 90.00
c = 96.370γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata scaling
AMoREphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2015-04-22
    Type: Database references