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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:30 UTC
Update Date2021-09-14 15:18:17 UTC
HMDB IDHMDB0001986
Secondary Accession Numbers
  • HMDB01986
Metabolite Identification
Common NameLacto-N-difucopentaose II
DescriptionLacto-N-difucopentaose II is an oligosaccharide first isolated from human milk by recycling chromatography in 1988. Is resistant to enzymic hydrolysis in the gastrointestinal tract of the infant; it is postulated that they reach the large intestine where they serve as substrates for bacterial metabolism. Oligosaccharides in human milk represent a group of bioactive molecules that have evolved to be an abundant and diverse component of human milk, even though they have no direct nutritive value to the infant. (PMID 3274083 , 10837303 , 11787695 , 14530096 , 17002410 ).
Structure
Data?1582752222
Synonyms
ValueSource
lacto-N-Difucohexaose IIHMDB
LNDFH IIHMDB
O-6-Deoxy-a-L-galactopyranosyl-(1->3)-O-[O-6-deoxy-a-L-galactopyranosyl-(1->4)-O-[b-D-galactopyranosyl-(1->3)]-O-2-(acetylamino)-2-deoxy-b-D-glucopyranosyl-(1->3)-b-D-galactopyranosyl-(1->4)]- D-glucoseHMDB
O-6-Deoxy-alpha-L-galactopyranosyl-(1->3)-O-[O-6-deoxy-alpha-L-galactopyranosyl-(1->4)-O-[b-D-galactopyranosyl-(1->3)]-O-2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl-(1->3)-beta-D-galactopyranosyl-(1->4)]- D-glucoseHMDB
O-6-Deoxy-alpha-L-galactopyranosyl-(1->3)-O-[O-6-deoxy-alpha-L-galactopyranosyl-(1->4)-O-[b-delta-galactopyranosyl-(1->3)]-O-2-(acetylamino)-2-deoxy-beta-delta-glucopyranosyl-(1->3)-beta-delta-galactopyranosyl-(1->4)]- D-glucoseHMDB
O-a-L-Fucopyranosyl-(1->4)-O-[b-D-galactopyranosyl-(1->3)]-O-2-acetamido-2-deoxy-b-D-glucopyranosyl-(1->3)-O-b-D-galactopyranosyl-(1->4)-O-[a-L-fucopyranosyl-(1->3)]- D-glucoseHMDB
O-alpha-L-Fucopyranosyl-(1->4)-O-[b-D-galactopyranosyl-(1->3)]-O-2-acetamido-2-deoxy-beta-D-glucopyranosyl-(1->3)-O-beta-D-galactopyranosyl-(1->4)-O-[a-L-fucopyranosyl-(1->3)]- D-glucoseHMDB
O-alpha-L-Fucopyranosyl-(1->4)-O-[b-delta-galactopyranosyl-(1->3)]-O-2-acetamido-2-deoxy-beta-delta-glucopyranosyl-(1->3)-O-beta-delta-galactopyranosyl-(1->4)-O-[a-L-fucopyranosyl-(1->3)]- D-glucoseHMDB
N-[(2S,3R,4R,5S,6R)-2-{[(2R,3S,4S,5R,6S)-3,5-dihydroxy-2-(hydroxymethyl)-6-{[(2R,3R,4R,5S)-1,2,5-trihydroxy-6-oxo-4-{[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}hexan-3-yl]oxy}oxan-4-yl]oxy}-6-(hydroxymethyl)-4-{[(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}oxan-3-yl]ethanimidateGenerator, HMDB
Chemical FormulaC38H65NO29
Average Molecular Weight999.912
Monoisotopic Molecular Weight999.364225123
IUPAC NameN-[(2S,3R,4R,5S,6R)-2-{[(2R,3S,4S,5R,6S)-3,5-dihydroxy-2-(hydroxymethyl)-6-{[(2R,3R,4R,5S)-1,2,5-trihydroxy-6-oxo-4-{[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}hexan-3-yl]oxy}oxan-4-yl]oxy}-6-(hydroxymethyl)-4-{[(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}oxan-3-yl]acetamide
Traditional NameN-[(2S,3R,4R,5S,6R)-2-{[(2R,3S,4S,5R,6S)-3,5-dihydroxy-2-(hydroxymethyl)-6-{[(2R,3R,4R,5S)-1,2,5-trihydroxy-6-oxo-4-{[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}hexan-3-yl]oxy}oxan-4-yl]oxy}-6-(hydroxymethyl)-4-{[(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}oxan-3-yl]acetamide
CAS Registry Number62258-12-2
SMILES
[H][C@@](O[C@@H]1O[C@H](CO)[C@H](O)[C@]([H])(O[C@@H]2O[C@H](CO)[C@@H](O[C@]3([H])O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]3O)[C@H](O[C@]3([H])O[C@H](CO)[C@H](O)[C@H](O)[C@H]3O)[C@H]2NC(C)=O)[C@H]1O)([C@H](O)CO)[C@]([H])(O[C@@H]1O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]1O)[C@H](O)C=O
InChI Identifier
InChI=1S/C38H65NO29/c1-9-18(48)22(52)25(55)35(59-9)64-29(12(46)4-40)30(13(47)5-41)65-38-28(58)33(21(51)15(7-43)62-38)68-34-17(39-11(3)45)32(67-37-27(57)24(54)20(50)14(6-42)61-37)31(16(8-44)63-34)66-36-26(56)23(53)19(49)10(2)60-36/h4,9-10,12-38,41-44,46-58H,5-8H2,1-3H3,(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 KeyQNSWVQWPVUZACH-ZQTNVGDNSA-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
  • Oxane
  • Fatty acyl
  • Alpha-hydroxyaldehyde
  • Acetamide
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Carboxamide group
  • Organoheterocyclic compound
  • Polyol
  • Acetal
  • Oxacycle
  • Carboxylic acid derivative
  • Alcohol
  • Organic oxide
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Carbonyl group
  • Organic nitrogen compound
  • Aldehyde
  • Primary alcohol
  • 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 Solubility128 g/LALOGPS
logP-2ALOGPS
logP-11ChemAxon
logS-0.89ALOGPS
pKa (Strongest Acidic)11.34ChemAxon
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
Polarizability93.61 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
AllCCS[M+H]+280.732859911
AllCCS[M+H-H2O]+281.532859911
AllCCS[M+NH4]+280.032859911
AllCCS[M+Na]+279.832859911
AllCCS[M-H]-319.032859911
AllCCS[M+Na-2H]-324.032859911
AllCCS[M+HCOO]-329.532859911

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 10V, Positive-QTOFsplash10-0080-0103002094-987d215b0546aecf1b902017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 20V, Positive-QTOFsplash10-0573-0506105292-c4c353adb70f057166e52017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 40V, Positive-QTOFsplash10-004u-2804019364-7bd6334e0a7f9c72b8212017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 10V, Negative-QTOFsplash10-001i-3111010149-36bb61502c0ba138818b2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 20V, Negative-QTOFsplash10-001i-3303223359-4a61a2f9dff985e0aa4e2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 40V, Negative-QTOFsplash10-03mi-6947551010-ff04384c76802dcb152e2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 10V, Positive-QTOFsplash10-0pe9-3309004042-7c114b64db76e1939d0b2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 20V, Positive-QTOFsplash10-0f7n-3902075432-7d020f22289150855b0c2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 40V, Positive-QTOFsplash10-0002-4901011010-353aff4549c3a20c0fca2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 10V, Negative-QTOFsplash10-0002-1000000029-fce0808c0342fbc045d22021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 20V, Negative-QTOFsplash10-052e-2400001009-ac04f25d564d866f70cf2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 40V, Negative-QTOFsplash10-08i9-6900004003-e9e52e2e8da3ac9d63522021-09-25Wishart 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
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
Breast MilkDetected and Quantified0.11 uMAdult (>18 years old)FemaleNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022783
KNApSAcK IDNot Available
Chemspider ID30776550
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53477740
PDB IDNot Available
ChEBI ID89338
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Engfer MB, Stahl B, Finke B, Sawatzki G, Daniel H: Human milk oligosaccharides are resistant to enzymatic hydrolysis in the upper gastrointestinal tract. Am J Clin Nutr. 2000 Jun;71(6):1589-96. [PubMed:10837303 ]
  2. Donald AS, Feeney J: Separation of human milk oligosaccharides by recycling chromatography. First isolation of lacto-N-neo-difucohexaose II and 3'-Galactosyllactose from this source. Carbohydr Res. 1988 Jul 15;178:79-91. [PubMed:3274083 ]
  3. Ninonuevo MR, Park Y, Yin H, Zhang J, Ward RE, Clowers BH, German JB, Freeman SL, Killeen K, Grimm R, Lebrilla CB: A strategy for annotating the human milk glycome. J Agric Food Chem. 2006 Oct 4;54(20):7471-80. [PubMed:17002410 ]
  4. Coppa GV, Pierani P, Zampini L, Bruni S, Carloni I, Gabrielli O: Characterization of oligosaccharides in milk and feces of breast-fed infants by high-performance anion-exchange chromatography. Adv Exp Med Biol. 2001;501:307-14. [PubMed:11787695 ]
  5. Von Seggern CE, Cotter RJ: Fragmentation studies of noncovalent sugar-sugar complexes by infrared atmospheric pressure MALDI. J Am Soc Mass Spectrom. 2003 Oct;14(10):1158-65. [PubMed:14530096 ]