Hmdb loader
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2007-05-24 12:18:38 UTC
Update Date2021-09-14 15:18:59 UTC
HMDB IDHMDB0006580
Secondary Accession Numbers
  • HMDB06580
Metabolite Identification
Common NameLacto-N-difucohexaose
DescriptionLacto-N-difucohexaose (LDFH) is a fucosyloligosaccharide present in human milk and colostrum. Human colostrum is known to be important for the protection of infants against infection by pathogenic microorganisms. This protection is thought to be due, partially, to various neutral and acidic oligosaccharides that are present in colostrum and milk. Moderate-to-severe diarrhea of all causes occurs less often in infants whose milk contains high levels of total 2-linked fucosyloligosaccharides as a percent of milk oligosaccharide. Calicivirus diarrhea occurs less often in infants whose mother's milk contains high levels of LDFH. (PMID: 15343178 , 17375110 , 12568665 ).
Structure
Data?1582752393
Synonyms
ValueSource
Lacto-N-difucohexaose IMeSH
LND 1HMDB
LND IHMDB
LNDFH-IHMDB
O-6-Deoxy-a-L-galactopyranosyl-(1->2)-O-b-D-galactopyranosyl-(1->3)-O-[6-deoxy-a-L-galactopyranosyl-(1->4)]-O-2-acetamido-2-deoxy-b-D-glucopyranosyl-(1->3)-O-b-D-galactopyranosyl-(1->4)-D-glucopyranoseHMDB
O-6-Deoxy-a-L-galactopyranosyl-(1->4)-O-[O-6-deoxy-a-L-galactopyranosyl-(1->2)-b-D-galactopyranosyl-(1->3)]-O-2-(acetylamino)-2-deoxy-b-D-glucopyranosyl-(1->3)-O-b-D-galactopyranosyl-(1->4)-D-glucoseHMDB
O-6-Deoxy-alpha-L-galactopyranosyl-(1->2)-O-beta-D-galactopyranosyl-(1->3)-O-[6-deoxy-alpha-L-galactopyranosyl-(1->4)]-O-2-acetamido-2-deoxy-beta-D-glucopyranosyl-(1->3)-O-beta-D-galactopyranosyl-(1->4)-D-glucopyranoseHMDB
O-6-Deoxy-alpha-L-galactopyranosyl-(1->4)-O-[O-6-deoxy-alpha-L-galactopyranosyl-(1->2)-beta-D-galactopyranosyl-(1->3)]-O-2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl-(1->3)-O-beta-D-galactopyranosyl-(1->4)-D-glucoseHMDB
N-[(2R,3R,4R,5S,6R)-2-{[(2R,3S,4R,5R)-4-{[(2R,3R,4S,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-2-yl]oxy}-6-hydroxy-1-oxo-2-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5-{[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}hexan-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl]ethanimidateGenerator, HMDB
Chemical FormulaC38H65NO29
Average Molecular Weight999.912
Monoisotopic Molecular Weight999.364225123
IUPAC NameN-[(2R,3R,4R,5S,6R)-2-{[(2R,3S,4R,5R)-4-{[(2R,3R,4S,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-2-yl]oxy}-6-hydroxy-1-oxo-2-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5-{[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}hexan-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl]acetamide
Traditional NameN-[(2R,3R,4R,5S,6R)-2-{[(2R,3S,4R,5R)-4-{[(2R,3R,4S,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-2-yl]oxy}-6-hydroxy-1-oxo-2-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5-{[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}hexan-3-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl]acetamide
CAS Registry Number16789-38-1
SMILES
C[C@@H]1O[C@@H](O[C@H](CO)[C@@H](O[C@H]2O[C@H](CO)[C@H](O)[C@H](O)[C@H]2O[C@@H]2O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]2O)[C@H](O[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2NC(C)=O)[C@@H](O[C@H]2O[C@H](CO)[C@H](O)[C@H](O)[C@H]2O)C=O)[C@@H](O)[C@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C38H65NO29/c1-9-18(46)24(52)28(56)35(59-9)64-16(8-44)32(67-38-33(27(55)22(50)14(6-42)63-38)68-36-29(57)25(53)19(47)10(2)60-36)31(15(7-43)65-37-30(58)26(54)21(49)13(5-41)62-37)66-34-17(39-11(3)45)23(51)20(48)12(4-40)61-34/h7,9-10,12-38,40-42,44,46-58H,4-6,8H2,1-3H3,(H,39,45)/t9-,10-,12+,13+,14+,15-,16+,17+,18+,19+,20+,21-,22-,23+,24+,25+,26-,27-,28-,29-,30+,31+,32+,33+,34+,35-,36-,37+,38+/m0/s1
InChI KeyPSJVAGXZRSPYJB-UUXGNFCPSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as oligosaccharides. These are carbohydrates made up of 3 to 10 monosaccharide units linked to each other through glycosidic bonds.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentOligosaccharides
Alternative Parents
Substituents
  • Oligosaccharide
  • Fatty acyl glycoside
  • N-acyl-alpha-hexosamine
  • Alkyl glycoside
  • Glycosyl compound
  • O-glycosyl compound
  • Fatty acyl
  • Oxane
  • Acetamide
  • Carboxamide group
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Acetal
  • Carboxylic acid derivative
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Hydrocarbon derivative
  • Organic oxide
  • Alcohol
  • Organopnictogen compound
  • Carbonyl group
  • Aldehyde
  • Primary alcohol
  • Organonitrogen compound
  • Organic nitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
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 Solubility175 g/LALOGPS
logP-2ALOGPS
logP-11ChemAxon
logS-0.76ALOGPS
pKa (Strongest Acidic)11.41ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count29ChemAxon
Hydrogen Donor Count18ChemAxon
Polar Surface Area482.38 ŲChemAxon
Rotatable Bond Count19ChemAxon
Refractivity207.43 m³·mol⁻¹ChemAxon
Polarizability93.21 ųChemAxon
Number of Rings5ChemAxon
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]+276.63830932474
DeepCCS[M-H]-274.91930932474
DeepCCS[M-2H]-308.95230932474
DeepCCS[M+Na]+282.79530932474
AllCCS[M+H]+279.432859911
AllCCS[M+H-H2O]+280.132859911
AllCCS[M+NH4]+278.832859911
AllCCS[M+Na]+278.632859911
AllCCS[M-H]-327.732859911
AllCCS[M+Na-2H]-332.732859911
AllCCS[M+HCOO]-338.332859911

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucohexaose 10V, Positive-QTOFsplash10-00el-1100027194-d0a3b1ed91774365d72a2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucohexaose 20V, Positive-QTOFsplash10-006x-0100039141-b5d6bef1b4aa3a7db72c2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucohexaose 40V, Positive-QTOFsplash10-01ox-4420059142-ee76e600a06c10e394d62017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucohexaose 10V, Negative-QTOFsplash10-01q9-2501015977-3b2eee873f6a3c9351522017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucohexaose 20V, Negative-QTOFsplash10-03e9-1910017136-e17831ccb3aecc7d98002017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucohexaose 40V, Negative-QTOFsplash10-03fr-3900011210-bd9426601aa6003518672017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucohexaose 10V, Positive-QTOFsplash10-0uei-5032003098-59e98a950bca4ac4f40d2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucohexaose 20V, Positive-QTOFsplash10-0uel-4902005252-cf0830c4aae88c6066482021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucohexaose 40V, Positive-QTOFsplash10-003g-9300010011-7b047c2c81810697928e2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucohexaose 10V, Negative-QTOFsplash10-0f6t-0100000139-747f2d69bfdd3bf7f31d2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucohexaose 20V, Negative-QTOFsplash10-0a4l-9601000058-3336b5b612d3d433f1432021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucohexaose 40V, Negative-QTOFsplash10-0a6u-9210055052-5780c2f57b0e2a457b122021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Breast Milk
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
Breast MilkDetected and Quantified0.550 uMAdult (>18 years old)FemaleNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedNewborn (0-30 days old)Not Specified
Premature neonates
details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023982
KNApSAcK IDNot Available
Chemspider ID2339585
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound3082109
PDB IDNot Available
ChEBI ID89922
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. Morrow AL, Ruiz-Palacios GM, Altaye M, Jiang X, Guerrero ML, Meinzen-Derr JK, Farkas T, Chaturvedi P, Pickering LK, Newburg DS: Human milk oligosaccharides are associated with protection against diarrhea in breast-fed infants. J Pediatr. 2004 Sep;145(3):297-303. [PubMed:15343178 ]
  2. Asakuma S, Urashima T, Akahori M, Obayashi H, Nakamura T, Kimura K, Watanabe Y, Arai I, Sanai Y: Variation of major neutral oligosaccharides levels in human colostrum. Eur J Clin Nutr. 2008 Apr;62(4):488-94. Epub 2007 Mar 21. [PubMed:17375110 ]
  3. Sumiyoshi W, Urashima T, Nakamura T, Arai I, Saito T, Tsumura N, Wang B, Brand-Miller J, Watanabe Y, Kimura K: Determination of each neutral oligosaccharide in the milk of Japanese women during the course of lactation. Br J Nutr. 2003 Jan;89(1):61-9. [PubMed:12568665 ]