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Record Information
Version2.0
Created at2022-09-06 20:02:22 UTC
Updated at2022-09-06 20:02:22 UTC
NP-MRD IDNP0237004
Secondary Accession NumbersNone
Natural Product Identification
Common Name(5z)-5-ethylidene-12-hydroxy-8,13-dimethoxy-3,9-diazatricyclo[8.4.0.0³,⁷]tetradeca-1(14),10,12-trien-2-one
DescriptionTomaymycin belongs to the class of organic compounds known as 1,4-benzodiazepines. These are organic compounds containing a benzene ring fused to a 1,4-azepine. (5z)-5-ethylidene-12-hydroxy-8,13-dimethoxy-3,9-diazatricyclo[8.4.0.0³,⁷]tetradeca-1(14),10,12-trien-2-one is found in Streptomyces achromogenes. (5z)-5-ethylidene-12-hydroxy-8,13-dimethoxy-3,9-diazatricyclo[8.4.0.0³,⁷]tetradeca-1(14),10,12-trien-2-one was first documented in 2008 (PMID: 18925745). Based on a literature review a significant number of articles have been published on Tomaymycin (PMID: 36061714) (PMID: 33973323) (PMID: 28890318) (PMID: 24761614) (PMID: 21809870) (PMID: 21488658).
Structure
Thumb
SynonymsNot Available
Chemical FormulaC16H20N2O4
Average Mass304.3460 Da
Monoisotopic Mass304.14231 Da
IUPAC NameNot Available
Traditional NameNot Available
CAS Registry NumberNot Available
SMILES
COC1NC2=CC(O)=C(OC)C=C2C(=O)N2C\C(CC12)=C/C
InChI Identifier
InChI=1S/C16H20N2O4/c1-4-9-5-12-15(22-3)17-11-7-13(19)14(21-2)6-10(11)16(20)18(12)8-9/h4,6-7,12,15,17,19H,5,8H2,1-3H3/b9-4-
InChI KeyUQVNRKBFAXNOGA-WTKPLQERSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Streptomyces achromogenesLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 1,4-benzodiazepines. These are organic compounds containing a benzene ring fused to a 1,4-azepine.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassBenzodiazepines
Sub Class1,4-benzodiazepines
Direct Parent1,4-benzodiazepines
Alternative Parents
Substituents
  • 1,4-benzodiazepine
  • Anisole
  • Phenol ether
  • Alkyl aryl ether
  • 1-hydroxy-2-unsubstituted benzenoid
  • Phenol
  • Benzenoid
  • Vinylogous amide
  • Tertiary carboxylic acid amide
  • Pyrrolidine
  • Carboxamide group
  • Lactam
  • Carboxylic acid derivative
  • Ether
  • Azacycle
  • Hydrocarbon derivative
  • Organic oxygen compound
  • Organic nitrogen compound
  • Organic oxide
  • Organonitrogen compound
  • Organooxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00018843
Chemspider ID4787755
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkTomaymycin
METLIN IDNot Available
PubChem Compound6039936
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Leitis ZR, Sakaine G, Kine Ns A, Smits G: Stereoselective Olefination with Sterically Demanding Julia-Kocienski Reagents: Total Synthesis of Oxo-prothracarcin, Oxo-tomaymycin, and Boseongazepine B. ACS Omega. 2022 Aug 17;7(34):30519-30534. doi: 10.1021/acsomega.2c03732. eCollection 2022 Aug 30. [PubMed:36061714 ]
  2. Aubert C, Lavisse M, Roy S: Biosynthesis of [(14) C]-11-De-O-Methyltomaymycin, a Precursor of Radiolabelled Antibody Drug Conjugates. Chembiochem. 2021 Jul 15;22(14):2424-2429. doi: 10.1002/cbic.202100080. Epub 2021 Jun 1. [PubMed:33973323 ]
  3. von Tesmar A, Hoffmann M, Pippel J, Fayad AA, Dausend-Werner S, Bauer A, Blankenfeldt W, Muller R: Total Biosynthesis of the Pyrrolo[4,2]benzodiazepine Scaffold Tomaymycin on an In Vitro Reconstituted NRPS System. Cell Chem Biol. 2017 Oct 19;24(10):1216-1227.e8. doi: 10.1016/j.chembiol.2017.08.001. Epub 2017 Sep 7. [PubMed:28890318 ]
  4. Liu B, Tan Y, Gan ML, Zhou HX, Wang YG, Ping YH, Li B, Yang ZY, Xiao CL: [Identification of tetracenomycin X from a marine-derived Saccharothrix sp. guided by genes sequence analysis]. Yao Xue Xue Bao. 2014 Feb;49(2):230-6. [PubMed:24761614 ]
  5. Burks EA, Yan W, Johnson WH Jr, Li W, Schroeder GK, Min C, Gerratana B, Zhang Y, Whitman CP: Kinetic, crystallographic, and mechanistic characterization of TomN: elucidation of a function for a 4-oxalocrotonate tautomerase homologue in the tomaymycin biosynthetic pathway. Biochemistry. 2011 Sep 6;50(35):7600-11. doi: 10.1021/bi200947w. Epub 2011 Aug 15. [PubMed:21809870 ]
  6. Hopton SR, Thompson AS: Nuclear magnetic resonance solution structures of inter- and intrastrand adducts of DNA cross-linker SJG-136. Biochemistry. 2011 May 31;50(21):4720-32. doi: 10.1021/bi102017e. Epub 2011 May 3. [PubMed:21488658 ]
  7. Li W, Chou S, Khullar A, Gerratana B: Cloning and characterization of the biosynthetic gene cluster for tomaymycin, an SJG-136 monomeric analog. Appl Environ Microbiol. 2009 May;75(9):2958-63. doi: 10.1128/AEM.02325-08. Epub 2009 Mar 6. [PubMed:19270147 ]
  8. Antonow D, Barata T, Jenkins TC, Parkinson GN, Howard PW, Thurston DE, Zloh M: Solution structure of a 2:1 C2-(2-naphthyl) pyrrolo[2,1-c][1,4]benzodiazepine DNA adduct: molecular basis for unexpectedly high DNA helix stabilization. Biochemistry. 2008 Nov 11;47(45):11818-29. doi: 10.1021/bi801225q. Epub 2008 Oct 17. [PubMed:18925745 ]
  9. LOTUS database [Link]