4M5K The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase date 2013-08-08
authors Yun, M., Hoagland, D., Kumar, G., Waddell, B., Rock, C.O., Lee, R.E., White, S.W.
compound source
symmetry
R_factor
R_Free 0.1743
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.30
ligand APC, CA, GOL, YH3 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe identification, analysis and structure-based development of novel inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase., Yun MK, Hoagland D, Kumar G, Waddell MB, Rock CO, Lee RE, White SW, Bioorg Med Chem. 2014 Apr 1;22(7):2157-65. doi: 10.1016/j.bmc.2014.02.022. Epub, 2014 Feb 25. PMID:24613625
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (62 Kb) [Save to disk]
  • Biological Unit Coordinates (4m5k.pdb1.gz) 57 Kb
  • LPC: Ligand-Protein Contacts for 4M5K
  • CSU: Contacts of Structural Units for 4M5K
  • Structure Factors (253 Kb)
  • Retrieve 4M5K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4M5K from S2C, [Save to disk]
  • Re-refined 4m5k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4M5K 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 4M5K
  • 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 4M5K, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4m5k] [4m5k_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4M5K
  • Community annotation for 4M5K at PDBWiki (http://pdbwiki.org)

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