2VX0 Transferase date Jun 30, 2008
title Ephb4 Kinase Domain Inhibitor Complex
authors J.Read, C.A.Brassington, I.Green, E.J.Mccall, A.L.Valentine, D.Barratt, A.G.Leach, J.G.Kettle
compound source
Molecule: Ephrin Type-B Receptor 4
Chain: A
Fragment: Kinase Domain, Residues 598-899
Synonym: Tyrosine-Protein Kinase Receptor Htk, Tyrosine-Pro Kinase Tyro11, Ephb4 Receptor Tyrosine Kinase;
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_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 0.18436 R_Free 0.23286
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.123 53.492 61.265 90.00 110.91 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand 7X7, MG BindingDB enzyme Transferase E.C.2.7.10.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceInhibitors of the tyrosine kinase EphB4. Part 1: Structure-based design and optimization of a series of 2,4-bis-anilinopyrimidines., Bardelle C, Cross D, Davenport S, Kettle JG, Ko EJ, Leach AG, Mortlock A, Read J, Roberts NJ, Robins P, Williams EJ, Bioorg Med Chem Lett. 2008 May 1;18(9):2776-80. Epub 2008 Apr 10. PMID:18434142
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (54 Kb) [Save to disk]
  • Biological Unit Coordinates (2vx0.pdb1.gz) 48 Kb
  • LPC: Ligand-Protein Contacts for 2VX0
  • CSU: Contacts of Structural Units for 2VX0
  • Likely Quarternary Molecular Structure file(s) for 2VX0
  • Structure Factors (119 Kb)
  • Retrieve 2VX0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VX0 from S2C, [Save to disk]
  • Re-refined 2vx0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VX0 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 2VX0
  • 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 2VX0, from MSDmotif at EBI
  • Fold representative 2vx0 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vx0] [2vx0_A]
  • SWISS-PROT database: [P54760]
  • Domain organization of [EPHB4_HUMAN] by SWISSPFAM
  • Domain found in 2VX0: [TyrKc ] by SMART
  • Alignments of the sequence of 2VX0 with the sequences similar proteins can be viewed for 2VX0's classification [EPHB4_HUMAN] 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 [EPHB4_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2VX0
  • Community annotation for 2VX0 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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