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Record Information
Version2.0
Created at2021-01-05 20:53:04 UTC
Updated at2021-07-15 17:07:53 UTC
NP-MRD IDNP0011074
Secondary Accession NumbersNone
Natural Product Identification
Common NameLomaiviticin C
Provided ByNPAtlasNPAtlas Logo
Description Lomaiviticin C is found in Salinispora pacifica. Lomaiviticin C was first documented in 2012 (PMID: 22963534). Based on a literature review very few articles have been published on (1R,2S,3R)-11-(diazyn-1-ium-1-yl)-1-{[(2R,4S,5R,6S)-5-(dimethylamino)-4-hydroxy-6-methyloxan-2-yl]oxy}-3-[(1R,2S,3S)-1-{[(2R,4S,5R,6S)-5-(dimethylamino)-4-hydroxy-6-methyloxan-2-yl]oxy}-2-ethyl-4,5,10-trihydroxy-2-{[(2R,4R,5R,6R)-5-hydroxy-4-methoxy-6-methyloxan-2-yl]oxy}-6,9-dioxo-1H,2H,3H,6H,9H-cyclohexa[b]fluoren-3-yl]-2-ethyl-5,10-dihydroxy-2-{[(2R,4R,5R,6R)-5-hydroxy-4-methoxy-6-methyloxan-2-yl]oxy}-4,9-dioxo-1H,2H,3H,4H,9H-cyclohexa[b]fluoren-6-olate (PMID: 30930633) (PMID: 33900077) (PMID: 28956437) (PMID: 24848236).
Structure
Thumb
Synonyms
ValueSource
(1R,2S,3R)-11-(Diazyn-1-ium-1-yl)-1-{[(2R,4S,5R,6S)-5-(dimethylamino)-4-hydroxy-6-methyloxan-2-yl]oxy}-3-[(1R,2S,3S)-1-{[(2R,4S,5R,6S)-5-(dimethylamino)-4-hydroxy-6-methyloxan-2-yl]oxy}-2-ethyl-4,5,10-trihydroxy-2-{[(2R,4R,5R,6R)-5-hydroxy-4-methoxy-6-methyloxan-2-yl]oxy}-6,9-dioxo-1H,2H,3H,6H,9H-cyclohexa[b]fluoren-3-yl]-2-ethyl-5,10-dihydroxy-2-{[(2R,4R,5R,6R)-5-hydroxy-4-methoxy-6-methyloxan-2-yl]oxy}-4,9-dioxo-1H,2H,3H,4H,9H-cyclohexa[b]fluoren-6-olic acidGenerator
Chemical FormulaC68H82N4O24
Average Mass1339.4080 Da
Monoisotopic Mass1338.53190 Da
IUPAC Name(1R,2S,3R)-1-{[(2R,4S,5R,6S)-5-(dimethylamino)-4-hydroxy-6-methyloxan-2-yl]oxy}-3-[(1R,2S,3S)-1-{[(2R,4S,5R,6S)-5-(dimethylamino)-4-hydroxy-6-methyloxan-2-yl]oxy}-2-ethyl-4,5,10-trihydroxy-2-{[(2R,4R,5R,6R)-5-hydroxy-4-methoxy-6-methyloxan-2-yl]oxy}-6,9-dioxo-1H,2H,3H,6H,9H-cyclohexa[b]fluoren-3-yl]-2-ethyl-5,10-dihydroxy-2-{[(2R,4R,5R,6R)-5-hydroxy-4-methoxy-6-methyloxan-2-yl]oxy}-11-(-lambda4,-lambda2-diazynylidene)-1H,2H,3H,4H,6H,9H,11H-cyclohexa[b]fluorene-4,6,9-trione
Traditional Name(1R,2S,3R)-1-{[(2R,4S,5R,6S)-5-(dimethylamino)-4-hydroxy-6-methyloxan-2-yl]oxy}-3-[(1R,2S,3S)-1-{[(2R,4S,5R,6S)-5-(dimethylamino)-4-hydroxy-6-methyloxan-2-yl]oxy}-2-ethyl-4,5,10-trihydroxy-2-{[(2R,4R,5R,6R)-5-hydroxy-4-methoxy-6-methyloxan-2-yl]oxy}-6,9-dioxo-1H,3H-cyclohexa[b]fluoren-3-yl]-2-ethyl-5,10-dihydroxy-2-{[(2R,4R,5R,6R)-5-hydroxy-4-methoxy-6-methyloxan-2-yl]oxy}-11-(-lambda4,-lambda2-diazynylidene)-1H,3H-cyclohexa[b]fluorene-4,6,9-trione
CAS Registry NumberNot Available
SMILES
CC[C@@]1(O[C@@H]2C[C@@H](OC)[C@H](O)[C@@H](C)O2)[C@H](O[C@@H]2C[C@H](O)[C@H]([C@H](C)O2)N(C)C)C2=CC3=C(C2=C(O)[C@@H]1[C@H]1C(=O)C2=C([C@@H](O[C@@H]4C[C@H](O)[C@H]([C@H](C)O4)N(C)C)[C@@]1(CC)O[C@@H]1C[C@@H](OC)[C@H](O)[C@@H](C)O1)C(=[N+]=[N-])C1=C2C(O)=C2C(=O)C=CC(=O)C2=C1O)C(O)=C1C(=O)C=CC(=O)C1=C3O
InChI Identifier
InChI=1S/C68H82N4O24/c1-13-67(95-40-22-36(87-11)57(79)26(5)91-40)52(63(85)43-29(65(67)93-38-20-34(77)55(71(7)8)24(3)89-38)19-28-42(43)60(82)45-31(74)16-15-30(73)44(45)59(28)81)53-64(86)49-48-50(62(84)47-33(76)18-17-32(75)46(47)61(48)83)54(70-69)51(49)66(94-39-21-35(78)56(72(9)10)25(4)90-39)68(53,14-2)96-41-23-37(88-12)58(80)27(6)92-41/h15-19,24-27,34-41,52-53,55-58,65-66,77-85H,13-14,20-23H2,1-12H3/t24-,25-,26+,27+,34-,35-,36+,37+,38+,39+,40+,41+,52-,53-,55-,56-,57+,58+,65+,66+,67-,68-/m0/s1
InChI KeyNZZSDJHUISSTSC-QIXKQXDESA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Salinispora pacificaNPAtlas
Chemical Taxonomy
ClassificationNot classified
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
logP2.81ALOGPS
logP1.85ChemAxon
logS-3.1ALOGPS
pKa (Strongest Acidic)6.18ChemAxon
pKa (Strongest Basic)8.43ChemAxon
Physiological Charge2ChemAxon
Hydrogen Acceptor Count27ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area383.27 ŲChemAxon
Rotatable Bond Count15ChemAxon
Refractivity339.87 m³·mol⁻¹ChemAxon
Polarizability138.79 ųChemAxon
Number of Rings12ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
NPAtlas IDNPA020334
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID78439869
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound136754226
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Woo CM, Beizer NE, Janso JE, Herzon SB: Isolation of lomaiviticins C-E, transformation of lomaiviticin C to lomaiviticin A, complete structure elucidation of lomaiviticin A, and structure-activity analyses. J Am Chem Soc. 2012 Sep 19;134(37):15285-8. doi: 10.1021/ja3074984. Epub 2012 Sep 10. [PubMed:22963534 ]
  2. Ozakin S, Ince E: Genome and metabolome mining of marine obligate Salinisporsatrains to discover new natural products. Turk J Biol. 2019 Feb 7;43(1):28-36. doi: 10.3906/biy-1807-136. eCollection 2019. [PubMed:30930633 ]
  3. Kim LJ, Xue M, Li X, Xu Z, Paulson E, Mercado B, Nelson HM, Herzon SB: Structure Revision of the Lomaiviticins. J Am Chem Soc. 2021 May 5;143(17):6578-6585. doi: 10.1021/jacs.1c01729. Epub 2021 Apr 26. [PubMed:33900077 ]
  4. Herzon SB: The Mechanism of Action of (-)-Lomaiviticin A. Acc Chem Res. 2017 Oct 17;50(10):2577-2588. doi: 10.1021/acs.accounts.7b00347. Epub 2017 Sep 28. [PubMed:28956437 ]
  5. Colis LC, Woo CM, Hegan DC, Li Z, Glazer PM, Herzon SB: The cytotoxicity of (-)-lomaiviticin A arises from induction of double-strand breaks in DNA. Nat Chem. 2014 Jun;6(6):504-10. doi: 10.1038/nchem.1944. Epub 2014 May 11. [PubMed:24848236 ]