5CEH Oxidoreductase Inhibitor date Jul 06, 2015
title Structure Of Histone Lysine Demethylase Kdm5a In Complex Wit Selective Inhibitor
authors J.R.Kiefer, M.Vinogradova
compound source
Molecule: Lysine-Specific Demethylase 5a
Chain: A
Fragment: Unp Residues 12-797
Synonym: Histone Demethylase Jarid1a,Jumonjiarid Domain-Co Protein 1a,Retinoblastoma-Binding Protein 2,Rbbp-2;
Ec: 1.14.11.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kdm5a, Jarid1a, Rbbp2, Rbp2
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_strain: Sf9
Expression_system_plasmid: Pacgp67

Molecule: Unknown Peptide
Chain: B
Engineered: Yes
Other_details: A Large Section Of Chain A Is Missing In The Coordinates And Chain B Is Probably A Part Of Chain A

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kdm5a, Jarid1a, Rbbp2, Rbp2
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_strain: Sf9
Expression_system_plasmid: Pacgp67
symmetry Space Group: P 31 2 1
R_factor 0.221 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
159.306 159.306 92.462 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.14 Å
ligand 50P, NI, ZN enzyme Oxidoreductase E.C.1.14.11 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceAn inhibitor of KDM5 demethylases reduces survival of drug-tolerant cancer cells., Vinogradova M, Gehling VS, Gustafson A, Arora S, Tindell CA, Wilson C, Williamson KE, Guler GD, Gangurde P, Manieri W, Busby J, Flynn EM, Lan F, Kim HJ, Odate S, Cochran AG, Liu Y, Wongchenko M, Yang Y, Cheung TK, Maile TM, Lau T, Costa M, Hegde GV, Jackson E, Pitti R, Arnott D, Bailey C, Bellon S, Cummings RT, Albrecht BK, Harmange JC, Kiefer JR, Trojer P, Classon M, Nat Chem Biol. 2016 Jul;12(7):531-8. doi: 10.1038/nchembio.2085. Epub 2016 May, 23. PMID:27214401
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (209 Kb) [Save to disk]
  • Biological Unit Coordinates (5ceh.pdb1.gz) 201 Kb
  • LPC: Ligand-Protein Contacts for 5CEH
  • CSU: Contacts of Structural Units for 5CEH
  • Structure Factors (382 Kb)
  • Retrieve 5CEH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5CEH from S2C, [Save to disk]
  • Re-refined 5ceh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5CEH 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 5CEH
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ceh] [5ceh_A] [5ceh_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5CEH: [ARID] [BRIGHT] [JmjC] [JmjN] [PHD ] by SMART
  • Other resources with information on 5CEH
  • Community annotation for 5CEH at PDBWiki (http://pdbwiki.org)

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