3WE4 Transferase Transferase Inhibitor date Jun 29, 2013
title Crystal Structure Of S6k1 Kinase Domain In Complex With A Py Derivative Pf-4708671 2-{[4-(5-Ethylpyrimidin-4-Yl)Piperazi Yl]Methyl}-5-(Trifluoromethyl)-1h-Benzimidazole
authors H.Niwa, M.Shirouzu, S.Yokoyama
compound source
Molecule: Ribosomal Protein S6 Kinase Beta-1
Chain: A
Fragment: Unp Residues 78-399
Synonym: S6k-Beta-1, S6k1, 70 Kda Ribosomal Protein S6 Kina Ribosomal Protein S6 Kinase I, Serinethreonine-Protein Kin P70 Ribosomal S6 Kinase Alpha;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rps6kb1
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 41 21 2
R_factor 0.175 R_Free 0.231
length a length b length c angle alpha angle beta angle gamma
70.930 70.930 146.861 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand 5FI, TPO, ZN enzyme Transferase E.C. BRENDA

Primary referenceCrystal structures of the S6K1 kinase domain in complexes with inhibitors., Niwa H, Mikuni J, Sasaki S, Tomabechi Y, Honda K, Ikeda M, Ohsawa N, Wakiyama M, Handa N, Shirouzu M, Honma T, Tanaka A, Yokoyama S, J Struct Funct Genomics. 2014 Sep;15(3):153-164. Epub 2014 Jul 31. PMID:25078151
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (107 Kb) [Save to disk]
  • Biological Unit Coordinates (3we4.pdb1.gz) 102 Kb
  • LPC: Ligand-Protein Contacts for 3WE4
  • CSU: Contacts of Structural Units for 3WE4
  • Structure Factors (1324 Kb)
  • Retrieve 3WE4 in mmCIF format [Save to disk]
  • Re-refined 3we4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3WE4 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 3WE4
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3WE4, from MSDmotif at EBI
  • Fold representative 3we4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3we4_A] [3we4]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3WE4: [S_TK_X] [S_TKc ] by SMART
  • Other resources with information on 3WE4
  • Community annotation for 3WE4 at PDBWiki (http://pdbwiki.org)

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