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Record Information
Version2.0
Created at2020-12-09 00:48:55 UTC
Updated at2021-07-15 16:46:54 UTC
NP-MRD IDNP0003615
Secondary Accession NumbersNone
Natural Product Identification
Common NamePacidamycin 4N
Provided ByNPAtlasNPAtlas Logo
Description2-({[1-({2-[1-(8-Hydroxy-1,2,3,4-tetrahydroisoquinolin-3-yl)-N-methylformamido]-1-({[(2Z)-4-hydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-ylidene]methyl}-C-hydroxycarbonimidoyl)propyl}-C-hydroxycarbonimidoyl)ethyl]-C-hydroxycarbonimidoyl}amino)-3-(1H-indol-3-yl)propanoic acid belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond. Pacidamycin 4N is found in Streptomyces coeruleorubidus. Based on a literature review very few articles have been published on 2-({[1-({2-[1-(8-hydroxy-1,2,3,4-tetrahydroisoquinolin-3-yl)-N-methylformamido]-1-({[(2Z)-4-hydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-ylidene]methyl}-C-hydroxycarbonimidoyl)propyl}-C-hydroxycarbonimidoyl)ethyl]-C-hydroxycarbonimidoyl}amino)-3-(1H-indol-3-yl)propanoic acid.
Structure
Thumb
Synonyms
ValueSource
2-({[1-({2-[1-(8-hydroxy-1,2,3,4-tetrahydroisoquinolin-3-yl)-N-methylformamido]-1-({[(2Z)-4-hydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-ylidene]methyl}-C-hydroxycarbonimidoyl)propyl}-C-hydroxycarbonimidoyl)ethyl]-C-hydroxycarbonimidoyl}amino)-3-(1H-indol-3-yl)propanoateGenerator
Chemical FormulaC39H45N9O11
Average Mass815.8410 Da
Monoisotopic Mass815.32385 Da
IUPAC Name(2S)-2-({[(1R)-1-{[(1R,2S)-1-({[(2Z,4S,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-4-hydroxyoxolan-2-ylidene]methyl}carbamoyl)-2-{1-[(3S)-8-hydroxy-1,2,3,4-tetrahydroisoquinolin-3-yl]-N-methylformamido}propyl]carbamoyl}ethyl]carbamoyl}amino)-3-(1H-indol-3-yl)propanoic acid
Traditional Name(2S)-2-({[(1R)-1-{[(1R,2S)-1-({[(2Z,4S,5R)-5-(2,4-dioxo-3H-pyrimidin-1-yl)-4-hydroxyoxolan-2-ylidene]methyl}carbamoyl)-2-{1-[(3S)-8-hydroxy-1,2,3,4-tetrahydroisoquinolin-3-yl]-N-methylformamido}propyl]carbamoyl}ethyl]carbamoyl}amino)-3-(1H-indol-3-yl)propanoic acid
CAS Registry NumberNot Available
SMILES
CC(NC(=O)NC(CC1=CNC2=CC=CC=C12)C(O)=O)C(=O)NC(C(C)N(C)C(=O)C1CC2=C(CN1)C(O)=CC=C2)C(=O)N\C=C1\CC(O)C(O1)N1C=CC(=O)NC1=O
InChI Identifier
InChI=1S/C39H45N9O11/c1-19(43-38(57)44-28(37(55)56)14-22-16-40-26-9-5-4-8-24(22)26)33(52)46-32(20(2)47(3)35(54)27-13-21-7-6-10-29(49)25(21)18-41-27)34(53)42-17-23-15-30(50)36(59-23)48-12-11-31(51)45-39(48)58/h4-12,16-17,19-20,27-28,30,32,36,40-41,49-50H,13-15,18H2,1-3H3,(H,42,53)(H,46,52)(H,55,56)(H2,43,44,57)(H,45,51,58)/b23-17-
InChI KeyCZFUSRPUOPGWDS-QJOMJCCJSA-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
Streptomyces coeruleorubidusNPAtlas
Species Where Detected
Species NameSourceReference
Streptomyces coeruleorubidus NRRL 18370KNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentDipeptides
Alternative Parents
Substituents
  • Alpha-dipeptide
  • N-acyl-alpha amino acid or derivatives
  • N-carbamoyl-alpha-amino acid
  • N-carbamoyl-alpha-amino acid or derivatives
  • Alpha-amino acid amide
  • Indolyl carboxylic acid derivative
  • Alanine or derivatives
  • N-substituted-alpha-amino acid
  • Alpha-amino acid or derivatives
  • Tetrahydroisoquinoline
  • 3-alkylindole
  • Indole
  • Indole or derivatives
  • 1-hydroxy-4-unsubstituted benzenoid
  • 1-hydroxy-2-unsubstituted benzenoid
  • Pyrimidone
  • Aralkylamine
  • Benzenoid
  • Fatty acyl
  • Fatty amide
  • Substituted pyrrole
  • Hydropyrimidine
  • N-acyl-amine
  • Pyrimidine
  • Vinylogous amide
  • Tetrahydrofuran
  • Tertiary carboxylic acid amide
  • Heteroaromatic compound
  • Pyrrole
  • Urea
  • Amino acid or derivatives
  • Carboxamide group
  • Secondary carboxylic acid amide
  • Lactam
  • Amino acid
  • Secondary alcohol
  • Carbonic acid derivative
  • Monocarboxylic acid or derivatives
  • Secondary amine
  • Organoheterocyclic compound
  • Carboxylic acid
  • Secondary aliphatic amine
  • Azacycle
  • Oxacycle
  • Alcohol
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Amine
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Carbonyl group
  • 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
logP0.98ALOGPS
logP-3.7ChemAxon
logS-4.2ALOGPS
pKa (Strongest Acidic)3.59ChemAxon
pKa (Strongest Basic)7.83ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area283.86 ŲChemAxon
Rotatable Bond Count13ChemAxon
Refractivity207.54 m³·mol⁻¹ChemAxon
Polarizability84.06 ųChemAxon
Number of Rings6ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
NPAtlas IDNPA013883
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID8051467
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound9875785
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References