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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 00:00:21 UTC
Update Date2022-03-07 02:55:52 UTC
HMDB IDHMDB0038673
Secondary Accession Numbers
  • HMDB38673
Metabolite Identification
Common NameLyciumin B
DescriptionLyciumin B is a weakly acidic compound (based on its pKa). Outside of the human body, lyciumin b has been detected, but not quantified in, a few different foods, such as coffee and coffee products, herbs and spices, and tea. This could make lyciumin b a potential biomarker for the consumption of these foods.
Structure
Data?1563863237
Synonyms
ValueSource
3,6,9,12-Tetrahydroxy-2-{[1-hydroxy-2-({hydroxy[1-(5-hydroxy-3,4-dihydro-2H-pyrrole-2-carbonyl)pyrrolidin-2-yl]methylidene}amino)-3-(1H-indol-3-yl)propylidene]amino}-11-(hydroxymethyl)-5-(propan-2-yl)-1,4,7,10,13-pentaazatricyclo[14.6.1.0¹⁷,²²]tricosa-3,6,9,12,16(23),17,19,21-octaene-14-carboxylateGenerator
Chemical FormulaC44H52N10O11
Average Molecular Weight896.9441
Monoisotopic Molecular Weight896.381702556
IUPAC Name11-(hydroxymethyl)-2-[3-(1H-indol-3-yl)-2-{[1-(5-oxopyrrolidine-2-carbonyl)pyrrolidin-2-yl]formamido}propanamido]-3,6,9,12-tetraoxo-5-(propan-2-yl)-1,4,7,10,13-pentaazatricyclo[14.6.1.0¹⁷,²²]tricosa-16(23),17(22),18,20-tetraene-14-carboxylic acid
Traditional Name11-(hydroxymethyl)-2-[3-(1H-indol-3-yl)-2-{[1-(5-oxopyrrolidine-2-carbonyl)pyrrolidin-2-yl]formamido}propanamido]-5-isopropyl-3,6,9,12-tetraoxo-1,4,7,10,13-pentaazatricyclo[14.6.1.0¹⁷,²²]tricosa-16(23),17(22),18,20-tetraene-14-carboxylic acid
CAS Registry Number125756-66-3
SMILES
CC(C)C1NC(=O)C(NC(=O)C(CC2=CNC3=C2C=CC=C3)NC(=O)C2CCCN2C(=O)C2CCC(=O)N2)N2C=C(CC(NC(=O)C(CO)NC(=O)CNC1=O)C(O)=O)C1=C2C=CC=C1
InChI Identifier
InChI=1S/C44H52N10O11/c1-22(2)36-41(61)46-19-35(57)48-31(21-55)39(59)50-30(44(64)65)17-24-20-54(32-11-6-4-9-26(24)32)37(42(62)51-36)52-38(58)29(16-23-18-45-27-10-5-3-8-25(23)27)49-40(60)33-12-7-15-53(33)43(63)28-13-14-34(56)47-28/h3-6,8-11,18,20,22,28-31,33,36-37,45,55H,7,12-17,19,21H2,1-2H3,(H,46,61)(H,47,56)(H,48,57)(H,49,60)(H,50,59)(H,51,62)(H,52,58)(H,64,65)
InChI KeyBWRVBFMWWHWLBW-UHFFFAOYSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as cyclic peptides. These are compounds containing a cyclic moiety bearing a peptide backbone.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentCyclic peptides
Alternative Parents
Substituents
  • Cyclic alpha peptide
  • Alpha-amino acid or derivatives
  • 3-alkylindole
  • Indole
  • Indole or derivatives
  • N-acylpyrrolidine
  • Pyrroline carboxylic acid or derivatives
  • Substituted pyrrole
  • Benzenoid
  • Pyrrole
  • Pyrrolidine
  • Heteroaromatic compound
  • Pyrroline
  • Tertiary carboxylic acid amide
  • Cyclic carboximidic acid
  • Lactim
  • Carboxamide group
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carboximidic acid derivative
  • Organoheterocyclic compound
  • Azacycle
  • Carboximidic acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Polyol
  • Organic oxide
  • Organopnictogen compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Organooxygen compound
  • Organic oxygen compound
  • Primary alcohol
  • Alcohol
  • Organic nitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
Role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.041 g/LALOGPS
logP0.99ALOGPS
logP-1.7ChemAxon
logS-4.3ALOGPS
pKa (Strongest Acidic)3.62ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count11ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area302.26 ŲChemAxon
Rotatable Bond Count10ChemAxon
Refractivity227.66 m³·mol⁻¹ChemAxon
Polarizability89.79 ųChemAxon
Number of Rings7ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+304.97330932474
DeepCCS[M-H]-303.07730932474
DeepCCS[M-2H]-336.47330932474
DeepCCS[M+Na]+310.81330932474
AllCCS[M+H]+280.732859911
AllCCS[M+H-H2O]+281.132859911
AllCCS[M+NH4]+280.332859911
AllCCS[M+Na]+280.232859911
AllCCS[M-H]-247.832859911
AllCCS[M+Na-2H]-252.632859911
AllCCS[M+HCOO]-257.832859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Lyciumin BCC(C)C1NC(=O)C(NC(=O)C(CC2=CNC3=C2C=CC=C3)NC(=O)C2CCCN2C(=O)C2CCC(=O)N2)N2C=C(CC(NC(=O)C(CO)NC(=O)CNC1=O)C(O)=O)C1=C2C=CC=C17723.9Standard polar33892256
Lyciumin BCC(C)C1NC(=O)C(NC(=O)C(CC2=CNC3=C2C=CC=C3)NC(=O)C2CCCN2C(=O)C2CCC(=O)N2)N2C=C(CC(NC(=O)C(CO)NC(=O)CNC1=O)C(O)=O)C1=C2C=CC=C15984.4Standard non polar33892256
Lyciumin BCC(C)C1NC(=O)C(NC(=O)C(CC2=CNC3=C2C=CC=C3)NC(=O)C2CCCN2C(=O)C2CCC(=O)N2)N2C=C(CC(NC(=O)C(CO)NC(=O)CNC1=O)C(O)=O)C1=C2C=CC=C18207.7Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lyciumin B 10V, Positive-QTOFsplash10-0ufr-0101472190-7291a6e33c4a505858532016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lyciumin B 20V, Positive-QTOFsplash10-0kai-5422950000-0c759aaa6793464136462016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lyciumin B 40V, Positive-QTOFsplash10-053s-7943010000-2fb1570b42503647d0282016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lyciumin B 10V, Negative-QTOFsplash10-00mk-0000100190-cad718cdf0675fd56f3b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lyciumin B 20V, Negative-QTOFsplash10-002b-4110200390-683150fdd98356db85d72016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lyciumin B 40V, Negative-QTOFsplash10-0l6u-9322024100-fc9c727d25f6e9f24af02016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lyciumin B 10V, Negative-QTOFsplash10-0002-0000000190-0d1a6cca61a9e49753a62021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lyciumin B 20V, Negative-QTOFsplash10-001i-4141119570-7d96c0fbb8a750d4ea1f2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lyciumin B 40V, Negative-QTOFsplash10-0006-9420101000-61bcbd15eab83d11af9b2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lyciumin B 10V, Positive-QTOFsplash10-0002-0001000090-7cd0afab0aaf97a329f92021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lyciumin B 20V, Positive-QTOFsplash10-001j-4300001390-b7177b89e4d996b284602021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lyciumin B 40V, Positive-QTOFsplash10-00di-9200210040-89783b8b1483ebfafb252021-09-23Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB018073
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound14430292
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .