2YKB Chaperone date May 26, 2011
title Tricyclic Series Of Hsp90 Inhibitors
authors A.Dupuy, F.Vallee
compound source
Molecule: Heat Shock Protein Hsp 90-Alpha
Chain: A
Fragment: N-Domain, Residues 18-233
Synonym: Heat Shock 86 Kda, Hsp 86, Hsp86, Renal Carcinoma Ny-Ren-38, Hsp90;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: I 2 2 2
R_factor 0.1994 R_Free 0.2411
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.348 90.627 98.638 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.93 Å
ligand YKB enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceTricyclic Series of Heat Shock Protein 90 (Hsp90) Inhibitors Part I: Discovery of Tricyclic Imidazo[4,5-c]pyridines as Potent Inhibitors of the Hsp90 Molecular Chaperone., Vallee F, Carrez C, Pilorge F, Dupuy A, Parent A, Bertin L, Thompson F, Ferrari P, Fassy F, Lamberton A, Thomas A, Arrebola R, Guerif S, Rohaut A, Certal V, Ruxer JM, Delorme C, Jouanen A, Dumas J, Grepin C, Combeau C, Goulaouic H, Dereu N, Mikol V, Mailliet P, Minoux H, J Med Chem. 2011 Oct 27;54(20):7206-19. Epub 2011 Oct 5. PMID:21972823
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (2ykb.pdb1.gz) 39 Kb
  • LPC: Ligand-Protein Contacts for 2YKB
  • CSU: Contacts of Structural Units for 2YKB
  • Structure Factors (419 Kb)
  • Retrieve 2YKB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YKB from S2C, [Save to disk]
  • Re-refined 2ykb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YKB 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 2YKB
  • 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 2YKB, from MSDmotif at EBI
  • Fold representative 2ykb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ykb] [2ykb_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 2YKB with the sequences similar proteins can be viewed for 2YKB'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 2YKB
  • Community annotation for 2YKB at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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