5LS6 Transferase Inhibitor date Aug 22, 2016
title Structure Of Human Polycomb Repressive Complex 2 (Prc2) With
authors Y.Zhang, N.Justin, S.Chen, J.Wilson, S.Gamblin
compound source
Molecule: Histone-Lysine N-Methyltransferase Ezh2,Histone-L Methyltransferase Ezh2,Histone-Lysine N-Methyltransferase E
Chain: A, D, G, J
Synonym: Enx-1,Enhancer Of Zeste Homolog 2,Lysine N-Methylt 6,Enx-1,Enhancer Of Zeste Homolog 2,Lysine N-Methyltransfer 1,Enhancer Of Zeste Homolog 2,Lysine N-Methyltransferase 6;
Ec: 2.1.1.43,2.1.1.43,2.1.1.43
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ezh2, Kmt6
Expression_system: Escherichia Coli K-12
Expression_system_taxid: 83333

Molecule: Polycomb Protein Eed
Chain: B, E, H, K
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 K-12
Expression_system_taxid: 83333

Molecule: Polycomb Protein Suz12
Chain: C, F, I, L
Synonym: Chromatin Precipitated E2f Target 9 Protein,Chet 9 Joined To Jazf1 Protein,Suppressor Of Zeste 12 Protein Homo
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Suz12, Chet9, Jjaz1, Kiaa0160
Expression_system: Escherichia Coli K-12
Expression_system_taxid: 83333

Molecule: Jarid2 K116me3
Chain: Q, R, S, T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.229 R_Free 0.299
crystal
cell
length a length b length c angle alpha angle beta angle gamma
131.310 170.270 275.540 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.47 Å
ligand 74D, M3L, ZN enzyme Transferase E.C.2.1.1.43 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, J, D, G


H, K, E, B


Primary referenceIdentification of (R)-N-((4-Methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-2-methyl-1-(1-(1 -(2,2,2-trifluoroethyl)piperidin-4-yl)ethyl)-1H-indole-3-carboxamide (CPI-1205), a Potent and Selective Inhibitor of Histone Methyltransferase EZH2, Suitable for Phase I Clinical Trials for B-Cell Lymphomas., Vaswani RG, Gehling VS, Dakin LA, Cook AS, Nasveschuk CG, Duplessis M, Iyer P, Balasubramanian S, Zhao F, Good AC, Campbell R, Lee C, Cantone N, Cummings RT, Normant E, Bellon SF, Albrecht BK, Harmange JC, Trojer P, Audia JE, Zhang Y, Justin N, Chen S, Wilson JR, Gamblin SJ, J Med Chem. 2016 Nov 10;59(21):9928-9941. Epub 2016 Oct 28. PMID:27739677
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (713 Kb) [Save to disk]
  • Biological Unit Coordinates (5ls6.pdb1.gz) 184 Kb
  • Biological Unit Coordinates (5ls6.pdb2.gz) 184 Kb
  • Biological Unit Coordinates (5ls6.pdb3.gz) 185 Kb
  • Biological Unit Coordinates (5ls6.pdb4.gz) 183 Kb
  • LPC: Ligand-Protein Contacts for 5LS6
  • CSU: Contacts of Structural Units for 5LS6
  • Structure Factors (5314 Kb)
  • Retrieve 5LS6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5LS6 from S2C, [Save to disk]
  • Re-refined 5ls6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5LS6 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 5LS6
  • 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: [5ls6] [5ls6_L] [5ls6_I] [5ls6_E] [5ls6_A] [5ls6_C] [5ls6_F] [5ls6_J] [5ls6_R] [5ls6_T] [5ls6_D] [5ls6_Q] [5ls6_H] [5ls6_K] [5ls6_S] [5ls6_B] [5ls6_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5LS6
  • Community annotation for 5LS6 at PDBWiki (http://pdbwiki.org)

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