2YDK Transferase date Mar 22, 2011
title Discovery Of Checkpoint Kinase Inhibitor Azd7762 By Structur Design And Optimization Of Thiophene Carboxamide Ureas
authors J.A.Read, J.Breed, H.Haye, E.Mccall, S.Rowsell, A.Vallentine, A.Wh
compound source
Molecule: Serinethreonine-Protein Kinase Chk1
Chain: A
Fragment: Chk1kd, Residues 1-276
Synonym: Chk1 Checkpoint Kinase
Ec: 2.7.11.1
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
symmetry Space Group: P 21 21 21
R_factor 0.181 R_Free 0.226
crystal
cell
length a length b length c angle alpha angle beta angle gamma
41.613 70.791 104.063 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand GOL, SO4, YDK BindingDB enzyme Transferase E.C.2.7.11.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceDiscovery of Checkpoint Kinase Inhibitor (S)-5-(3-fluorophenyl)-N-(piperidin-3-yl)-3-ureidothiophene-2-carboxamide (AZD7762) by Structure Based Design and Optimization of Thiophene Carboxamide Ureas., Oza VB, Ashwell S, Almeida L, Brassil P, Breed J, Deng C, Gero T, Grondine M, Horn C, Ioannidis S, Liu D, Lyne PD, Newcombe N, Pass M, Read J, Ready S, Rowsell S, Su M, Toader D, Vasbinder M, Yu D, Yu Y, Xue Y, Zabludoff S, Janetka J, J Med Chem. 2012 May 2. PMID:22551018
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (98 Kb) [Save to disk]
  • Biological Unit Coordinates (2ydk.pdb1.gz) 92 Kb
  • LPC: Ligand-Protein Contacts for 2YDK
  • CSU: Contacts of Structural Units for 2YDK
  • Structure Factors (307 Kb)
  • Retrieve 2YDK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YDK from S2C, [Save to disk]
  • Re-refined 2ydk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YDK 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 2YDK
  • 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
  • 3D motif for 2YDK, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ydk_A] [2ydk]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2YDK: [S_TKc ] by SMART
  • Other resources with information on 2YDK
  • Community annotation for 2YDK at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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