Np mrd loader

You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on NP-MRD.
Record Information
Version1.0
Created at2021-01-06 07:00:47 UTC
Updated at2021-07-15 17:37:08 UTC
NP-MRD IDNP0021739
Secondary Accession NumbersNone
Natural Product Identification
Common NameNucleocidin
Provided ByNPAtlasNPAtlas Logo
DescriptionNucleocidin is also known as antibiotic T-3018. Nucleocidin is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Nucleocidin is found in Streptomyces calvus and Streptomyces sp.. It was first documented in 1969 (PMID: 5776261). Based on a literature review a significant number of articles have been published on Nucleocidin (PMID: 32110306) (PMID: 30641108) (PMID: 28920128) (PMID: 28049355).
Structure
Data?1624506923
Synonyms
ValueSource
4'-C-Fluoroadenosine 5'-sulfamateChEBI
4'-Fluoro-5'-O-sulfamoyladenosineChEBI
4'-Fluoro-5'-O-sulphamoyladenosineChEBI
[(2S,3S,4R,5R)-5-(6-Amino-9H-purin-9-yl)-2-fluoro-3,4-dihydroxytetrahydrofuran-2-yl]methyl sulfamateChEBI
[(2S,3S,4R,5R)-5-(6-Aminopurin-9-yl)-2-fluoro-3,4-dihydroxyoxolan-2-yl]methyl sulfamateChEBI
Antibiotic T-3018ChEBI
T-3018ChEBI
4'-C-Fluoroadenosine 5'-sulfamic acidGenerator
4'-C-Fluoroadenosine 5'-sulphamateGenerator
4'-C-Fluoroadenosine 5'-sulphamic acidGenerator
[(2S,3S,4R,5R)-5-(6-Amino-9H-purin-9-yl)-2-fluoro-3,4-dihydroxytetrahydrofuran-2-yl]methyl sulfamic acidGenerator
[(2S,3S,4R,5R)-5-(6-Amino-9H-purin-9-yl)-2-fluoro-3,4-dihydroxytetrahydrofuran-2-yl]methyl sulphamateGenerator
[(2S,3S,4R,5R)-5-(6-Amino-9H-purin-9-yl)-2-fluoro-3,4-dihydroxytetrahydrofuran-2-yl]methyl sulphamic acidGenerator
[(2S,3S,4R,5R)-5-(6-Aminopurin-9-yl)-2-fluoro-3,4-dihydroxyoxolan-2-yl]methyl sulfamic acidGenerator
[(2S,3S,4R,5R)-5-(6-Aminopurin-9-yl)-2-fluoro-3,4-dihydroxyoxolan-2-yl]methyl sulphamateGenerator
[(2S,3S,4R,5R)-5-(6-Aminopurin-9-yl)-2-fluoro-3,4-dihydroxyoxolan-2-yl]methyl sulphamic acidGenerator
Chemical FormulaC10H13FN6O6S
Average Mass364.3100 Da
Monoisotopic Mass364.06013 Da
IUPAC Name[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-2-fluoro-3,4-dihydroxyoxolan-2-yl]methyl sulfamate
Traditional Name[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-2-fluoro-3,4-dihydroxyoxolan-2-yl]methyl sulfamate
CAS Registry NumberNot Available
SMILES
NC1=NC=NC2=C1N=CN2[C@@H]1O[C@](F)(COS(N)(=O)=O)[C@@H](O)[C@H]1O
InChI Identifier
InChI=1S/C10H13FN6O6S/c11-10(1-22-24(13,20)21)6(19)5(18)9(23-10)17-3-16-4-7(12)14-2-15-8(4)17/h2-3,5-6,9,18-19H,1H2,(H2,12,14,15)(H2,13,20,21)/t5-,6+,9-,10-/m1/s1
InChI KeyLTBCQBSAWAZBDF-MLTZYSBQSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 50 MHz, Acetone-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 150 MHz, Acetone-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 250 MHz, Acetone-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 175 MHz, Acetone-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, Acetone-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 100 MHz, Acetone-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 225 MHz, Acetone-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 200 MHz, Acetone-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 125 MHz, Acetone-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 25 MHz, Acetone-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, Acetone-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, Acetone-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, Acetone-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, Acetone-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, Acetone-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, Acetone-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, Acetone-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, Acetone-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, Acetone-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, Acetone-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
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
Streptomyces calvusLOTUS Database
Streptomyces sp.NPAtlas
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
logP-0.47ALOGPS
logP-2ChemAxon
logS-1.9ALOGPS
pKa (Strongest Acidic)10.93ChemAxon
pKa (Strongest Basic)3.92ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area188.7 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity74.81 m³·mol⁻¹ChemAxon
Polarizability30.51 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
NPAtlas IDNPA011799
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID65250
KEGG Compound IDNot Available
BioCyc IDCPD-12712
BiGG IDNot Available
Wikipedia LinkNucleocidin
METLIN IDNot Available
PubChem Compound72299
PDB IDNot Available
ChEBI ID166872
Good Scents IDNot Available
References
General References
  1. Feng X, Bello D, Lowe PT, Clark J, O'Hagan D: Two 3'-O-beta-glucosylated nucleoside fluorometabolites related to nucleocidin in Streptomyces calvus. Chem Sci. 2019 Aug 20;10(41):9501-9505. doi: 10.1039/c9sc03374b. eCollection 2019 Nov 7. [PubMed:32110306 ]
  2. Morton GO, Lancaster JE, Van Lear GE, Fulmor W, Meyer WE: The structure of nucleocidin. 3. (A new structure). J Am Chem Soc. 1969 Mar 12;91(6):1535-7. doi: 10.1021/ja01034a046. [PubMed:5776261 ]
  3. Zhang S, Klementz D, Zhu J, Makitrynskyy R, Ola Pasternak AR, Gunther S, Zechel DL, Bechthold A: Genome mining reveals the origin of a bald phenotype and a cryptic nucleocidin gene cluster in Streptomyces asterosporus DSM 41452. J Biotechnol. 2019 Feb 20;292:23-31. doi: 10.1016/j.jbiotec.2018.12.016. Epub 2019 Jan 11. [PubMed:30641108 ]
  4. Feng X, Al Maharik N, Bartholome A, Janso JE, Reilly U, O'Hagan D: Incorporation of [(2)H1]-(1R,2R)- and [(2)H1]-(1S,2R)-glycerols into the antibiotic nucleocidin in Streptomyces calvus. Org Biomol Chem. 2017 Oct 4;15(38):8006-8008. doi: 10.1039/c7ob02163a. [PubMed:28920128 ]
  5. Carvalho MF, Oliveira RS: Natural production of fluorinated compounds and biotechnological prospects of the fluorinase enzyme. Crit Rev Biotechnol. 2017 Nov;37(7):880-897. doi: 10.1080/07388551.2016.1267109. Epub 2017 Jan 3. [PubMed:28049355 ]