5FP3 Oxidoreductase date Nov 27, 2015
title Cell Penetrant Inhibitors Of The Jmjd2 (Kdm4) And Jarid1 (Kd Families Of Histone Lysine Demethylases
authors C.Chung
compound source
Molecule: Human Lysine-Specific Demethylase 6b, Jmjd3
Chain: A, B
Fragment: Catalytic Domain, Unp Residues 1141-1643
Synonym: Jmjc Domain-Containing Protein 3, Jumonji Domain-C Protein 3, Lysine Demethylase 6b, Jmjd3;
Ec: 1.14.11.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 1
R_factor 0.205 R_Free 0.243
crystal
cell
length a length b length c angle alpha angle beta angle gamma
61.199 65.552 77.301 85.59 67.65 68.39
method X-Ray Diffractionresolution 2.05 Å
ligand BCN, CO, MG, YC8, ZN enzyme Oxidoreductase E.C.1.14.11 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCell Penetrant Inhibitors of the KDM4 and KDM5 Families of Histone Lysine Demethylases. 1. 3-Amino-4-pyridine Carboxylate Derivatives., Westaway SM, Preston AG, Barker MD, Brown F, Brown JA, Campbell M, Chung CW, Diallo H, Douault C, Drewes G, Eagle R, Gordon L, Haslam C, Hayhow TG, Humphreys PG, Joberty G, Katso R, Kruidenier L, Leveridge M, Liddle J, Mosley J, Muelbaier M, Randle R, Rioja I, Rueger A, Seal GA, Sheppard RJ, Singh O, Taylor J, Thomas P, Thomson D, Wilson DM, Lee K, Prinjha RK, J Med Chem. 2016 Jan 15. PMID:26771107
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (305 Kb) [Save to disk]
  • Biological Unit Coordinates (5fp3.pdb1.gz) 154 Kb
  • Biological Unit Coordinates (5fp3.pdb2.gz) 147 Kb
  • LPC: Ligand-Protein Contacts for 5FP3
  • CSU: Contacts of Structural Units for 5FP3
  • Structure Factors (661 Kb)
  • Retrieve 5FP3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5FP3 from S2C, [Save to disk]
  • Re-refined 5fp3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5FP3 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 5FP3
  • 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: [5fp3_A] [5fp3] [5fp3_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5FP3: [JmjC ] by SMART
  • Other resources with information on 5FP3
  • Community annotation for 5FP3 at PDBWiki (http://pdbwiki.org)

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