4KB8 Transferase Transferase Inhibitor date Apr 23, 2013
title Ck1d In Complex With 1-{4-[3-(4-Fluorophenyl)-1-Methyl-1h-Py Yl]Pyridin-2-Yl}-N-Methylmethanamine Ligand
authors S.Liu
compound source
Molecule: Casein Kinase I Isoform Delta
Chain: A, B, C, D
Synonym: Cki-Delta, Ckid, Tau-Protein Kinase Csnk1d
Ec: 2.7.11.1, 2.7.11.26
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Csnk1d, Hckid
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
symmetry Space Group: P 1
R_factor 0.205 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
49.014 84.541 89.515 107.90 105.87 93.08
method X-Ray Diffractionresolution 1.95 Å
ligand 1QN, 1QO, SO4 enzyme Transferase E.C.2.7.11.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceLigand-protein interactions of selective casein kinase 1delta inhibitors., Mente S, Arnold E, Butler T, Chakrapani S, Chandrasekaran R, Cherry K, Dirico K, Doran A, Fisher K, Galatsis P, Green M, Hayward M, Humphrey J, Knafels J, Li J, Liu S, Marconi M, McDonald S, Ohren J, Paradis V, Sneed B, Walton K, Wager T, J Med Chem. 2013 Sep 12;56(17):6819-28. doi: 10.1021/jm4006324. Epub 2013 Aug 28. PMID:23919824
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (395 Kb) [Save to disk]
  • Biological Unit Coordinates (4kb8.pdb1.gz) 94 Kb
  • Biological Unit Coordinates (4kb8.pdb2.gz) 103 Kb
  • Biological Unit Coordinates (4kb8.pdb3.gz) 100 Kb
  • Biological Unit Coordinates (4kb8.pdb4.gz) 101 Kb
  • Biological Unit Coordinates (4kb8.pdb5.gz) 193 Kb
  • Biological Unit Coordinates (4kb8.pdb6.gz) 197 Kb
  • LPC: Ligand-Protein Contacts for 4KB8
  • CSU: Contacts of Structural Units for 4KB8
  • Structure Factors (1714 Kb)
  • Retrieve 4KB8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4KB8 from S2C, [Save to disk]
  • Re-refined 4kb8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4KB8 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 4KB8
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4KB8, from MSDmotif at EBI
  • Fold representative 4kb8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4kb8_C] [4kb8_B] [4kb8] [4kb8_A] [4kb8_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4KB8: [STYKc ] by SMART
  • Other resources with information on 4KB8
  • Community annotation for 4KB8 at PDBWiki (http://pdbwiki.org)

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