3U6J Transferase Transferase Inhibitor date Oct 12, 2011
title Crystal Structure Of The Vegfr2 Kinase Domain In Complex Wit Pyrazolone Inhibitor
authors D.A.Whittington, A.Long, P.Rose, Y.Gu, H.Zhao
compound source
Molecule: Vascular Endothelial Growth Factor Receptor 2
Chain: A
Fragment: Unp Residues 815-1171
Synonym: Vegfr-2, Fetal Liver Kinase 1, Flk-1, Kinase Inser Receptor, Protein-Tyrosine Kinase Receptor Flk-1;
Ec: 2.7.10.1
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Flk1, Kdr
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 1 21 1
R_factor 0.193 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.194 65.268 57.323 90.00 117.94 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand 03X BindingDB enzyme Transferase E.C.2.7.10.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure-Based Design of Novel Class II c-Met Inhibitors: 1. Identification of Pyrazolone-Based Derivatives., Norman MH, Liu L, Lee M, Xi N, Fellows I, D'Angelo ND, Dominguez C, Rex K, Bellon SF, Kim TS, Dussault I, J Med Chem. 2012 Feb 24. PMID:22320343
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (110 Kb) [Save to disk]
  • Biological Unit Coordinates (3u6j.pdb1.gz) 105 Kb
  • LPC: Ligand-Protein Contacts for 3U6J
  • CSU: Contacts of Structural Units for 3U6J
  • Structure Factors (493 Kb)
  • Retrieve 3U6J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3U6J from S2C, [Save to disk]
  • Re-refined 3u6j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3U6J in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3U6J
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3U6J, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3u6j] [3u6j_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3U6J: [TyrKc ] by SMART
  • Other resources with information on 3U6J
  • Community annotation for 3U6J at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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