3BYM Transferase date Jan 16, 2008
title X-Ray Co-Crystal Structure Aminobenzimidazole Triazine 1 Bou
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: Baculovirus
Expression_system_cell_line: Insect Cell
symmetry Space Group: P 21 21 21
R_factor 0.226 R_Free 0.274
crystal
cell
length a length b length c angle alpha angle beta angle gamma
42.346 73.537 92.110 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand AM0, 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] (56 Kb) [Save to disk]
  • Biological Unit Coordinates (3bym.pdb1.gz) 52 Kb
  • LPC: Ligand-Protein Contacts for 3BYM
  • CSU: Contacts of Structural Units for 3BYM
  • Likely Quarternary Molecular Structure file(s) for 3BYM
  • Retrieve 3BYM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BYM from S2C, [Save to disk]
  • View 3BYM 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 3BYM
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3BYM, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bym_A] [3bym]
  • SWISS-PROT database: [P06239]
  • Domain organization of [LCK_HUMAN] by SWISSPFAM
  • Domain found in 3BYM: [TyrKc ] by SMART
  • Other resources with information on 3BYM
  • Community annotation for 3BYM 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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