Np mrd loader

Record Information
Version2.0
Created at2022-09-05 15:15:52 UTC
Updated at2022-09-05 15:15:52 UTC
NP-MRD IDNP0215595
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-[(2s,3s,6r)-3-[(2-amino-1,3-dihydroxypropylidene)amino]-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2,4-dihydroxypentanoic acid
DescriptionMildiomycin belongs to the class of organic compounds known as gamma amino acids and derivatives. These are amino acids having a (-NH2) group attached to the gamma carbon atom. It was first documented in 2008 (PMID: 18412191). Based on a literature review a significant number of articles have been published on Mildiomycin (PMID: 22753012) (PMID: 28000775) (PMID: 24920828) (PMID: 23659472).
Structure
Thumb
SynonymsNot Available
Chemical FormulaC19H30N8O9
Average Mass514.4960 Da
Monoisotopic Mass514.21357 Da
IUPAC Name2-[(2S,3S,6R)-3-[(2-amino-1,3-dihydroxypropylidene)amino]-6-[2-hydroxy-5-(hydroxymethyl)-4-imino-1,4-dihydropyrimidin-1-yl]-3,6-dihydro-2H-pyran-2-yl]-5-carbamimidamido-2,4-dihydroxypentanoic acid
Traditional Name2-[(2S,3S,6R)-3-[(2-amino-1,3-dihydroxypropylidene)amino]-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2H-pyran-2-yl]-5-carbamimidamido-2,4-dihydroxypentanoic acid
CAS Registry NumberNot Available
SMILES
NC(CO)C(O)=N[C@H]1C=C[C@@H](O[C@@H]1C(O)(CC(O)CNC(N)=N)C(O)=O)N1C=C(CO)C(=N)N=C1O
InChI Identifier
InChI=1S/C19H30N8O9/c20-10(7-29)15(31)25-11-1-2-12(27-5-8(6-28)14(21)26-18(27)34)36-13(11)19(35,16(32)33)3-9(30)4-24-17(22)23/h1-2,5,9-13,28-30,35H,3-4,6-7,20H2,(H,25,31)(H,32,33)(H2,21,26,34)(H4,22,23,24)/t9?,10?,11-,12+,13-,19?/m0/s1
InChI KeyQKJJCZYFXJCKRX-AMYGDCFASA-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 OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as gamma amino acids and derivatives. These are amino acids having a (-NH2) group attached to the gamma carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentGamma amino acids and derivatives
Alternative Parents
Substituents
  • Alpha-amino acid amide
  • Serine or derivatives
  • Gamma amino acid or derivatives
  • Alpha-amino acid or derivatives
  • Aminopyrimidine
  • Pyrimidone
  • Alpha-hydroxy acid
  • Hydropyrimidine
  • Hydroxy acid
  • Pyran
  • Pyrimidine
  • Imidolactam
  • Heteroaromatic compound
  • Tertiary alcohol
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Carboxamide group
  • Amino acid
  • Guanidine
  • Propargyl-type 1,3-dipolar organic compound
  • Carboximidamide
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organic 1,3-dipolar compound
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Aromatic alcohol
  • Organic oxygen compound
  • Organic nitrogen compound
  • Primary aliphatic amine
  • Organonitrogen compound
  • Organooxygen compound
  • Primary alcohol
  • Carbonyl group
  • Primary amine
  • Organic oxide
  • Alcohol
  • Amine
  • Hydrocarbon derivative
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic 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
logP-8.3ChemAxon
pKa (Strongest Acidic)2.76ChemAxon
pKa (Strongest Basic)11.38ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count17ChemAxon
Hydrogen Donor Count12ChemAxon
Polar Surface Area307.64 ŲChemAxon
Rotatable Bond Count11ChemAxon
Refractivity142.75 m³·mol⁻¹ChemAxon
Polarizability49.84 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00018185
Chemspider ID8025063
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound9849350
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Wu J, Li L, Deng Z, Zabriskie TM, He X: Analysis of the mildiomycin biosynthesis gene cluster in Streptoverticillum remofaciens ZJU5119 and characterization of MilC, a hydroxymethyl cytosyl-glucuronic acid synthase. Chembiochem. 2012 Jul 23;13(11):1613-21. doi: 10.1002/cbic.201200173. Epub 2012 Jun 29. [PubMed:22753012 ]
  2. Zhao G, Chen C, Xiong W, Gao T, Deng Z, Wu G, He X: Structural basis of the substrate preference towards CMP for a thymidylate synthase MilA involved in mildiomycin biosynthesis. Sci Rep. 2016 Dec 21;6:39675. doi: 10.1038/srep39675. [PubMed:28000775 ]
  3. Zhao G, Wu G, Zhang Y, Liu G, Han T, Deng Z, He X: Structure of the N-glycosidase MilB in complex with hydroxymethyl CMP reveals its Arg23 specifically recognizes the substrate and controls its entry. Nucleic Acids Res. 2014 Jul;42(12):8115-24. doi: 10.1093/nar/gku486. Epub 2014 Jun 11. [PubMed:24920828 ]
  4. Sikowitz MD, Cooper LE, Begley TP, Kaminski PA, Ealick SE: Reversal of the substrate specificity of CMP N-glycosidase to dCMP. Biochemistry. 2013 Jun 11;52(23):4037-47. doi: 10.1021/bi400316p. Epub 2013 May 28. [PubMed:23659472 ]
  5. Li L, Xu Z, Xu X, Wu J, Zhang Y, He X, Zabriskie TM, Deng Z: The mildiomycin biosynthesis: initial steps for sequential generation of 5-hydroxymethylcytidine 5'-monophosphate and 5-hydroxymethylcytosine in Streptoverticillium rimofaciens ZJU5119. Chembiochem. 2008 May 23;9(8):1286-94. doi: 10.1002/cbic.200800008. [PubMed:18412191 ]
  6. LOTUS database [Link]