Hmdb loader
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:36:58 UTC
Update Date2022-03-07 02:52:33 UTC
HMDB IDHMDB0030466
Secondary Accession Numbers
  • HMDB30466
Metabolite Identification
Common NameGoldinodox
DescriptionGoldinodox, also known as antibiotic X 5108 or aurodox, belongs to the class of organic compounds known as c-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a C-glycosidic bond. Based on a literature review very few articles have been published on Goldinodox.
Structure
Data?1563861990
Synonyms
ValueSource
1-Methylmocimycin, 9ciHMDB
Antibiotic X 5108HMDB
ANTIBIOTIC X-5108HMDB
AurodoxHMDB
GoldinomycinHMDB
MAUHMDB
N-Methyl kirromycinHMDB
X 5108HMDB
N-[(2Z,4E)-7-{3,4-dihydroxy-5-[(1Z,3E,5Z)-7-(4-hydroxy-1-methyl-2-oxo-1,2-dihydropyridin-3-yl)-6-methyl-7-oxohepta-1,3,5-trien-1-yl]oxolan-2-yl}-6-methoxy-5-methylocta-2,4-dien-1-yl]-2-{2,3,4-trihydroxy-5,5-dimethyl-6-[(1E,3Z)-penta-1,3-dien-1-yl]oxan-2-yl}butanimidateHMDB
N MethylkirromycinHMDB
N-MethylkirromycinHMDB
Chemical FormulaC44H62N2O12
Average Molecular Weight810.9693
Monoisotopic Molecular Weight810.430275458
IUPAC NameN-[(2Z,4E)-7-{3,4-dihydroxy-5-[(1Z,3E,5Z)-7-(4-hydroxy-1-methyl-2-oxo-1,2-dihydropyridin-3-yl)-6-methyl-7-oxohepta-1,3,5-trien-1-yl]oxolan-2-yl}-6-methoxy-5-methylocta-2,4-dien-1-yl]-2-{2,3,4-trihydroxy-5,5-dimethyl-6-[(1E,3Z)-penta-1,3-dien-1-yl]oxan-2-yl}butanamide
Traditional NameN-[(2Z,4E)-7-{3,4-dihydroxy-5-[(1Z,3E,5Z)-7-(4-hydroxy-1-methyl-2-oxopyridin-3-yl)-6-methyl-7-oxohepta-1,3,5-trien-1-yl]oxolan-2-yl}-6-methoxy-5-methylocta-2,4-dien-1-yl]-2-{2,3,4-trihydroxy-5,5-dimethyl-6-[(1E,3Z)-penta-1,3-dien-1-yl]oxan-2-yl}butanamide
CAS Registry Number12704-90-4
SMILES
CCC(C(=O)NC\C=C/C=C(\C)C(OC)C(C)C1OC(\C=C/C=C/C=C(/C)C(=O)C2=C(O)C=CN(C)C2=O)C(O)C1O)C1(O)OC(\C=C\C=C/C)C(C)(C)C(O)C1O
InChI Identifier
InChI=1S/C44H62N2O12/c1-10-12-14-22-32-43(6,7)39(51)40(52)44(55,58-32)29(11-2)41(53)45-24-18-17-20-27(4)37(56-9)28(5)38-36(50)35(49)31(57-38)21-16-13-15-19-26(3)34(48)33-30(47)23-25-46(8)42(33)54/h10,12-23,25,28-29,31-32,35-40,47,49-52,55H,11,24H2,1-9H3,(H,45,53)/b12-10-,15-13+,18-17-,21-16-,22-14+,26-19-,27-20+
InChI KeyNTAHMPNXQOYXSX-NJWHXGCDSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as c-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a C-glycosidic bond.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentC-glycosyl compounds
Alternative Parents
Substituents
  • C-glycosyl compound
  • Aryl ketone
  • Pyridinone
  • Hydroxypyridine
  • Dihydropyridine
  • Monosaccharide
  • N-acyl-amine
  • Oxane
  • Hydropyridine
  • Pyridine
  • Alpha-branched alpha,beta-unsaturated-ketone
  • Fatty acyl
  • Fatty amide
  • Alpha,beta-unsaturated ketone
  • Tetrahydrofuran
  • Vinylogous acid
  • Vinylogous amide
  • Acryloyl-group
  • Enone
  • Heteroaromatic compound
  • Carboxamide group
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Ketone
  • Hemiacetal
  • Lactam
  • Carboxylic acid derivative
  • Dialkyl ether
  • Oxacycle
  • Ether
  • Azacycle
  • Organoheterocyclic compound
  • Polyol
  • Alcohol
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Carbonyl group
  • Organic oxide
  • Organic nitrogen compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot Available
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 Solubility0.007 g/LALOGPS
logP4.23ALOGPS
logP3.5ChemAxon
logS-5.1ALOGPS
pKa (Strongest Acidic)8.12ChemAxon
pKa (Strongest Basic)-2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area215.55 ŲChemAxon
Rotatable Bond Count17ChemAxon
Refractivity227.78 m³·mol⁻¹ChemAxon
Polarizability86.6 ųChemAxon
Number of Rings3ChemAxon
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]+276.2530932474
DeepCCS[M-H]-274.42530932474
DeepCCS[M-2H]-308.17930932474
DeepCCS[M+Na]+281.97730932474
AllCCS[M+H]+288.332859911
AllCCS[M+H-H2O]+287.732859911
AllCCS[M+NH4]+288.832859911
AllCCS[M+Na]+288.932859911
AllCCS[M-H]-280.132859911
AllCCS[M+Na-2H]-287.032859911
AllCCS[M+HCOO]-294.532859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.4.57 minutes32390414
Predicted by Siyang on May 30, 202220.2445 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.68 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid4766.3 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid143.0 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid239.5 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid151.5 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid159.7 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid868.3 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid643.6 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)110.3 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1805.0 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid908.2 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid2142.2 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid609.6 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid620.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate119.6 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA130.8 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water10.9 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
GoldinodoxCCC(C(=O)NC\C=C/C=C(\C)C(OC)C(C)C1OC(\C=C/C=C/C=C(/C)C(=O)C2=C(O)C=CN(C)C2=O)C(O)C1O)C1(O)OC(\C=C\C=C/C)C(C)(C)C(O)C1O7453.2Standard polar33892256
GoldinodoxCCC(C(=O)NC\C=C/C=C(\C)C(OC)C(C)C1OC(\C=C/C=C/C=C(/C)C(=O)C2=C(O)C=CN(C)C2=O)C(O)C1O)C1(O)OC(\C=C\C=C/C)C(C)(C)C(O)C1O4594.4Standard non polar33892256
GoldinodoxCCC(C(=O)NC\C=C/C=C(\C)C(OC)C(C)C1OC(\C=C/C=C/C=C(/C)C(=O)C2=C(O)C=CN(C)C2=O)C(O)C1O)C1(O)OC(\C=C\C=C/C)C(C)(C)C(O)C1O5944.4Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Goldinodox GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-10-19Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Goldinodox GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-10-19Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Goldinodox GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-10-19Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Goldinodox GC-MS (TMS_1_4) - 70eV, PositiveNot Available2021-10-19Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Goldinodox GC-MS (TMS_1_5) - 70eV, PositiveNot Available2021-10-19Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Goldinodox GC-MS (TMS_1_6) - 70eV, PositiveNot Available2021-10-19Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Goldinodox GC-MS (TMS_1_7) - 70eV, PositiveNot Available2021-10-19Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Goldinodox 10V, Positive-QTOFsplash10-004i-6900000410-d950513c6d5b68f8db6c2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Goldinodox 20V, Positive-QTOFsplash10-0fbc-9712413400-34372573d7adefd4ea842016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Goldinodox 40V, Positive-QTOFsplash10-0fb9-9200100000-45f46dc5ee522a88f0222016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Goldinodox 10V, Negative-QTOFsplash10-00e9-0900000000-bc4b116be6d161c6ae9e2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Goldinodox 20V, Negative-QTOFsplash10-00di-1900010100-5a17009a605cedd820912016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Goldinodox 40V, Negative-QTOFsplash10-00di-4900000000-663d4416b250081e692c2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Goldinodox 10V, Positive-QTOFsplash10-01pn-0343900110-84be14ca1af91702bacc2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Goldinodox 20V, Positive-QTOFsplash10-0f83-2480823910-cb44dfd315d5162a901c2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Goldinodox 40V, Positive-QTOFsplash10-0uk9-2940200000-a6cb37e4161a99a8be6e2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Goldinodox 10V, Negative-QTOFsplash10-0006-0059020130-9d118a546ac5b39be4f92021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Goldinodox 20V, Negative-QTOFsplash10-0zfr-0192100100-27910dfa77b80e9620e32021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Goldinodox 40V, Negative-QTOFsplash10-0frf-5393171010-9b6bfe11d536f16059562021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Membrane
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 IDFDB002335
KNApSAcK IDC00018857
Chemspider ID35013205
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound137185903
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.. .