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;
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 0.17510 R_Free 0.20913
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. BRENDA
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] (100 Kb) [Save to disk]
  • Biological Unit Coordinates (2xvd.pdb1.gz) 94 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
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2XVD, from MSDmotif at EBI
  • Fold representative 2xvd from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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
  • Alignments of the sequence of 2XVD with the sequences similar proteins can be viewed for 2XVD's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • 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.

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