3ARA Hydrolase Hydrolase Inhibitor date Nov 25, 2010
title Discovery Of Novel Uracil Derivatives As Potent Human Dutpas Inhibitors
authors K.T.Chong, H.Miyakoshi, S.Miyahara, M.Fukuoka
compound source
Molecule: Deoxyuridine 5'-Triphosphate Nucleotidohydrolase
Chain: A, B, C
Synonym: Dut-N, Dutpase, Dutp Pyrophosphatase
Ec: 3.6.1.23
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet19b
symmetry Space Group: P 21 21 21
R_factor 0.214 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
81.890 83.263 89.662 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand MG, MKH BindingDB enzyme Hydrolase E.C.3.6.1.23 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceSynthesis and discovery of N-carbonylpyrrolidine- or N-sulfonylpyrrolidine-containing uracil derivatives as potent human deoxyuridine triphosphatase inhibitors., Miyakoshi H, Miyahara S, Yokogawa T, Chong KT, Taguchi J, Endoh K, Yano W, Wakasa T, Ueno H, Takao Y, Nomura M, Shuto S, Nagasawa H, Fukuoka M, J Med Chem. 2012 Apr 12;55(7):2960-9. Epub 2012 Mar 26. PMID:22404301
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (74 Kb) [Save to disk]
  • Biological Unit Coordinates (3ara.pdb1.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 3ARA
  • CSU: Contacts of Structural Units for 3ARA
  • Structure Factors (1206 Kb)
  • Retrieve 3ARA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ARA from S2C, [Save to disk]
  • Re-refined 3ara structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ARA 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 3ARA
  • 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 3ARA, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ara_A] [3ara_C] [3ara_B] [3ara]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3ARA
  • Community annotation for 3ARA at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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