5NHY Hydrolase date Mar 22, 2017
title Bay-707 In Complex With Mth1
authors M.Ellermann, A.Eheim, A.Giese, S.Bunse, K.Nowak-Reppel, R.Neuhaus J.Weiske, M.Quanz, A.Glasauer, H.Meyer, N.Queisser, H.Irlbacher, F.Rahm, J.Viklund, M.Andersson, U.Ericsson, T.Ginman, R.Forsblom J.Lindstrom, C.Silvander, L.Tresaugues, M.Gorjanacz
compound source
Molecule: 7,8-Dihydro-8-Oxoguanine Triphosphatase
Chain: A, B
Synonym: 2-Hydroxy-Datp Diphosphatase,8-Oxo-Dgtpase,Nucleos Diphosphate-Linked Moiety X Motif 1,Nudix Motif 1;
Ec: 3.6.1.55,3.6.1.56
Engineered: Yes
Other_details: Full Length Human Mth1 Isoform P18 Containin Residuals From A Thrombin-Cleavage Site In N-Terminus
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Variant: Isoform P18
Gene: Nudt1, Mth1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta Phage Resistant
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-28a
symmetry Space Group: P 21 21 21
R_factor 0.220 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
59.528 66.709 82.075 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.72 Å
ligand 8XT, GOL, SO4 enzyme Hydrolase E.C.3.6.1.55 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceNovel Class of Potent and Cellularly Active Inhibitors Devalidates MTH1 as Broad-Spectrum Cancer Target., Ellermann M, Eheim A, Rahm F, Viklund J, Guenther J, Andersson M, Ericsson U, Forsblom R, Ginman T, Lindstrom J, Silvander C, Tresaugues L, Giese A, Bunse S, Neuhaus R, Weiske J, Quanz M, Glasauer A, Nowak-Reppel K, Bader B, Irlbacher H, Meyer H, Queisser N, Bauser M, Haegebarth A, Gorjanacz M, ACS Chem Biol. 2017 Aug 18;12(8):1986-1992. doi: 10.1021/acschembio.7b00370. Epub, 2017 Jul 12. PMID:28679043
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (116 Kb) [Save to disk]
  • Biological Unit Coordinates (5nhy.pdb1.gz) 56 Kb
  • Biological Unit Coordinates (5nhy.pdb2.gz) 55 Kb
  • LPC: Ligand-Protein Contacts for 5NHY
  • CSU: Contacts of Structural Units for 5NHY
  • Structure Factors (1376 Kb)
  • Retrieve 5NHY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5NHY from S2C, [Save to disk]
  • Re-refined 5nhy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5NHY 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 5NHY
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5nhy_A] [5nhy_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5NHY
  • Community annotation for 5NHY at PDBWiki (http://pdbwiki.org)

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