2VIP Hydrolase date Dec 05, 2007
title Fragment-Based Discovery Of Mexiletine Derivatives As Orally Bioavailable Inhibitors Of Urokinase-Type Plasminogen Activ
authors M.Frederickson, O.Callaghan, G.Chessari, M.Congreve, S.R.Cowan, J.E.Matthews, R.Mcmenamin, D.Smith, M.Vinkovic, N.G.Wallis
compound source
Molecule: Urokinase-Type Plasminogen Activator Chain B
Chain: A
Fragment: Catalytic Domain, Residues 179-431
Synonym: Urokinase-Type Plasminogen Activator, Upa, U-Plasm Activator;
Ec: 3.4.21.73
Engineered: Yes
Mutation: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.162 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.488 54.382 81.029 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.72 Å
ligand ACT, L1R, SO4 BindingDB enzyme Hydrolase E.C.3.4.21.73 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceFragment-based discovery of mexiletine derivatives as orally bioavailable inhibitors of urokinase-type plasminogen activator., Frederickson M, Callaghan O, Chessari G, Congreve M, Cowan SR, Matthews JE, McMenamin R, Smith DM, Vinkovic M, Wallis NG, J Med Chem. 2008 Jan 24;51(2):183-6. Epub 2007 Dec 29. PMID:18163548
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (56 Kb) [Save to disk]
  • Biological Unit Coordinates (2vip.pdb1.gz) 50 Kb
  • LPC: Ligand-Protein Contacts for 2VIP
  • CSU: Contacts of Structural Units for 2VIP
  • Likely Quarternary Molecular Structure file(s) for 2VIP
  • Structure Factors (267 Kb)
  • Retrieve 2VIP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VIP from S2C, [Save to disk]
  • Re-refined 2vip structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2VIP 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 2VIP
  • 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 2VIP, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vip_A] [2vip]
  • SWISS-PROT database: [P00749]
  • Domain organization of [UROK_HUMAN] by SWISSPFAM
  • Domain found in 2VIP: [Tryp_SPc ] by SMART
    • Other resources with information on 2VIP
  • Community annotation for 2VIP 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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