2XVD Transferase date Oct 25, 2010
title Ephb4 Kinase Domain Inhibitor Complex
authors J.Read, C.A.Brassington, I.Green, E.J.Mccall, A.L.Valentine
compound source
Molecule: Ephrin Type-B Receptor 4
Chain: A
Fragment: Kinase Domain, Residues 598-899
Synonym: Tyrosine-Protein Kinase Tyro11, Tyrosine-Protein K Receptor Htk;
Ec: 2.7.10.1
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf21
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac
symmetry Space Group: P 1 21 1
R_factor 0.175 R_Free 0.209
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.708 53.315 61.330 90.00 111.75 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand AS6, MG BindingDB enzyme Transferase E.C.2.7.10.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceInhibitors of the tyrosine kinase EphB4. Part 4: Discovery and optimization of a benzylic alcohol series., Barlaam B, Ducray R, Lambert-van der Brempt C, Ple P, Bardelle C, Brooks N, Coleman T, Cross D, Kettle JG, Read J, Bioorg Med Chem Lett. 2011 Apr 15;21(8):2207-11. PMID:21441027
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (98 Kb) [Save to disk]
  • Biological Unit Coordinates (2xvd.pdb1.gz) 92 Kb
  • LPC: Ligand-Protein Contacts for 2XVD
  • CSU: Contacts of Structural Units for 2XVD
  • Structure Factors (349 Kb)
  • Retrieve 2XVD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XVD from S2C, [Save to disk]
  • Re-refined 2xvd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2XVD 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 2XVD
  • 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 2XVD, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xvd_A] [2xvd]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2XVD: [TyrKc ] by SMART
  • Other resources with information on 2XVD
  • Community annotation for 2XVD at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science