5U6D Protein Binding, Inhibitor date Dec 07, 2016
title Polycomb Protein Eed In Complex With Inhibitor: 2-[4-(4-{(3s (Dimethylamino)-1-[(2-Fluoro-6-Methylphenyl)Methyl]Pyrrolid Yl}Phenyl)-1h-Pyrazol-1-Yl]Acetamide
authors C.G.Jakob, H.Zhu
compound source
Molecule: Polycomb Protein Eed
Chain: A
Synonym: Heed,Wd Protein Associating With Integrin Cytoplas 1,Wait-1;
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Eed
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.148 R_Free 0.178
crystal
cell
length a length b length c angle alpha angle beta angle gamma
57.663 85.161 91.711 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.64 Å
ligand 7XG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceSAR of amino pyrrolidines as potent and novel protein-protein interaction inhibitors of the PRC2 complex through EED binding., Curtin ML, Pliushchev MA, Li HQ, Torrent M, Dietrich JD, Jakob CG, Zhu H, Zhao H, Wang Y, Ji Z, Clark RF, Sarris KA, Selvaraju S, Shaw B, Algire MA, He Y, Richardson PL, Sweis RF, Sun C, Chiang GG, Michaelides MR, Bioorg Med Chem Lett. 2017 Apr 1;27(7):1576-1583. doi:, 10.1016/j.bmcl.2017.02.030. Epub 2017 Feb 20. PMID:28254486
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (130 Kb) [Save to disk]
  • Biological Unit Coordinates (5u6d.pdb1.gz) 125 Kb
  • LPC: Ligand-Protein Contacts for 5U6D
  • CSU: Contacts of Structural Units for 5U6D
  • Structure Factors (848 Kb)
  • Retrieve 5U6D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5U6D from S2C, [Save to disk]
  • Re-refined 5u6d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5U6D 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 5U6D
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5u6d] [5u6d_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5U6D
  • Community annotation for 5U6D at PDBWiki (http://pdbwiki.org)

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