3BYO Transferase date Jan 16, 2008
title X-Ray Co-Crystal Structure Of 2-Amino-6-Phenylpyrimido[5',4' 6]Pyrimido[1,2-A]Benzimidazol-5(6h)-One 25 Bound To Lck
authors X.Huang
compound source
Molecule: Proto-Oncogene Tyrosine-Protein Kinase Lck
Chain: A
Fragment: Kinase Domain
Synonym: P56-Lck, Lymphocyte Cell-Specific Protein-Tyrosine Lsk, T Cell-Specific Protein-Tyrosine Kinase;
Ec: 2.7.10.2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lck
Expression_system: Unidentified Baculovirus
Expression_system_taxid: 10469
Expression_system_cell_line: Insect Cell
symmetry Space Group: P 21 21 21
R_factor 0.223 R_Free 0.259
crystal
cell
length a length b length c angle alpha angle beta angle gamma
42.134 73.544 92.668 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand AM9, PTR, SO4 BindingDB enzyme Transferase E.C.2.7.10.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure-based design of novel 2-amino-6-phenyl-pyrimido[5',4':5,6]pyrimido[1,2-a]benzimidazol-5(6H)-ones as potent and orally active inhibitors of lymphocyte specific kinase (Lck): synthesis, SAR, and in vivo anti-inflammatory activity., Martin MW, Newcomb J, Nunes JJ, Boucher C, Chai L, Epstein LF, Faust T, Flores S, Gallant P, Gore A, Gu Y, Hsieh F, Huang X, Kim JL, Middleton S, Morgenstern K, Oliveira-dos-Santos A, Patel VF, Powers D, Rose P, Tudor Y, Turci SM, Welcher AA, Zack D, Zhao H, Zhu L, Zhu X, Ghiron C, Ermann M, Johnston D, Saluste CG, J Med Chem. 2008 Mar 27;51(6):1637-48. Epub 2008 Feb 16. PMID:18278858
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (54 Kb) [Save to disk]
  • Biological Unit Coordinates (3byo.pdb1.gz) 50 Kb
  • LPC: Ligand-Protein Contacts for 3BYO
  • CSU: Contacts of Structural Units for 3BYO
  • Likely Quarternary Molecular Structure file(s) for 3BYO
  • Structure Factors (553 Kb)
  • Retrieve 3BYO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BYO from S2C, [Save to disk]
  • Re-refined 3byo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BYO 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 3BYO
  • 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 3BYO, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3byo_A] [3byo]
  • SWISS-PROT database: [P06239]
  • Domain organization of [LCK_HUMAN] by SWISSPFAM
  • Domain found in 3BYO: [TyrKc ] by SMART
  • Other resources with information on 3BYO
  • Community annotation for 3BYO 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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