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Human Metabolome Database Version 3.5

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Showing metabocard for Pectin (HMDB03402)

Record Information
Version 3.5
Creation Date 2006-08-12 14:13:01 -0600
Update Date 2013-02-08 17:12:30 -0700
HMDB ID HMDB03402
Secondary Accession Numbers None
Metabolite Identification
Common Name Pectin
Description Pectin is a heterosaccharide derived from the cell wall of plants. Pectins vary in their chain lengths, complexity and the order of each of the monosaccharide units. The characteristic structure of pectin is a linear chain of alpha(1-4)linked D-galacturonic acid that forms the pectin-backbone, a homogalacturonan.
Structure Thumb
Download: MOL | SDF | SMILES | InChI
Display: 2D Structure | 3D Structure
Synonyms
  1. (+)-Xylose
  2. 2,3,4,5-Tetrahydroxypentanal
  3. D-Lyxose
  4. DL-Xylose
  5. L(+)-Xylose
  6. L-Lyxose
  7. Lyxose
  8. Pectin
  9. Pectin sugar
  10. Pectinose
  11. Pentose
  12. Trobicin
Chemical Formula C6H10O7
Average Molecular Weight 194.1394
Monoisotopic Molecular Weight 194.042652674
IUPAC Name (2S,3R,4S,5R,6R)-3,4,5,6-tetrahydroxyoxane-2-carboxylic acid
Traditional IUPAC Name β-D-galacturonic acid
CAS Registry Number 9000-69-5
SMILES O[C@@H]1O[C@@H]([C@H](O)[C@H](O)[C@H]1O)C(O)=O
InChI Identifier InChI=1S/C6H10O7/c7-1-2(8)4(5(10)11)13-6(12)3(1)9/h1-4,6-9,12H,(H,10,11)/t1-,2+,3+,4-,6+/m0/s1
InChI Key AEMOLEFTQBMNLQ-DTEWXJGMSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Carbohydrates and Carbohydrate Conjugates
Class Sugar Acids and Derivatives
Sub Class Glucuronic Acid Derivatives
Other Descriptors
  • Aliphatic Heteromonocyclic Compounds
  • Carbohydrates and Carbohydrate Conjugates
  • D-galactopyranuronic acid(ChEBI)
  • Glucuronic Acid Derivatives
Substituents
  • 1,2 Diol
  • Beta Hydroxy Acid
  • Carboxylic Acid
  • Hemiacetal
  • Hexose Monosaccharide
  • Oxane
  • Secondary Alcohol
Direct Parent Glucuronides
Ontology
Status Detected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Purine metabolism
  • Component of Pyrimidine metabolism
Application Not Available
Cellular locations
  • Extracellular
  • Lysosome
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point Not Available Not Available
Boiling Point Not Available Not Available
Water Solubility Not Available Not Available
LogP Not Available Not Available
Predicted Properties
Property Value Source
Water Solubility 295 g/L ALOGPS
LogP -2.30 ALOGPS
LogP -2.6 ChemAxon
LogS 0.18 ALOGPS
pKa (strongest acidic) 3.21 ChemAxon
pKa (strongest basic) -3.7 ChemAxon
Hydrogen Acceptor Count 7 ChemAxon
Hydrogen Donor Count 5 ChemAxon
Polar Surface Area 127.45 A2 ChemAxon
Rotatable Bond Count 1 ChemAxon
Refractivity 35.79 ChemAxon
Polarizability 16.34 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge -1 ChemAxon
Spectra
MS/MS Spectrum Quattro_QQQ 10
MS/MS Spectrum Quattro_QQQ 25
MS/MS Spectrum Quattro_QQQ 40
[1H,1H] 2D NMR Spectrum
[1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Lysosome
Biofluid Locations
  • Urine
Tissue Location
  • Skeletal Muscle
  • Bladder
  • Fibroblasts
  • Neuron
  • Placenta
  • Testes
  • Kidney
  • Epidermis
  • Prostate
  • Adipose Tissue
  • Platelet
  • Spleen
  • Small Intestine
Pathways Not Available
Normal Concentrations
Biofluid Status Value Age Sex Condition Reference
Urine Detected and Quantified
5.26 (4.0-7.0) umol/mmol creatinine Adult (>18 years old) Both Normal
  • Geigy Scient...
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease References None
Associated OMIM IDs None
DrugBank ID Not Available
DrugBank Metabolite ID Not Available
Phenol Explorer Compound ID Not Available
Phenol Explorer Metabolite ID Not Available
FoodDB ID FDB023162
KNApSAcK ID Not Available
Chemspider ID 390200 Link_out
KEGG Compound ID C08348 Link_out
BioCyc ID PECTIN Link_out
BiGG ID 34162 Link_out
Wikipedia Link Pectin Link_out
NuGOwiki Link HMDB03402 Link_out
Metagene Link HMDB03402 Link_out
METLIN ID 6916 Link_out
PubChem Compound 441476 Link_out
PDB ID GTR Link_out
ChEBI ID 47954 Link_out
References
Synthesis Reference Gu, Qu-Ming; Nickol, Robert G.; Cheng, H. N. Enzyme-catalyzed modification of pectin. Polymer Preprints (American Chemical Society, Division of Polymer Chemistry) (2003), 44(2), 608-609.
Material Safety Data Sheet (MSDS) Download (PDF)
General References
  1. Andoh A, Bamba T, Sasaki M: Physiological and anti-inflammatory roles of dietary fiber and butyrate in intestinal functions. JPEN J Parenter Enteral Nutr. 1999 Sep-Oct;23(5 Suppl):S70-3. Pubmed: 10483900 Link_out
  2. Fleming SE, Marthinsen D, Kuhnlein H: Colonic function and fermentation in men consuming high fiber diets. J Nutr. 1983 Dec;113(12):2535-44. Pubmed: 6317826 Link_out
  3. Lewinska D, Rosinski S, Piatkiewicz W: A new pectin-based material for selective LDL-cholesterol removal. Artif Organs. 1994 Mar;18(3):217-22. Pubmed: 8185488 Link_out
  4. Kelsay JL, Goering HK, Behall KM, Prather ES: Effect of fiber from fruits and vegetables on metabolic responses of human subjects: fiber intakes, fecal excretions, and apparent digestibilities. Am J Clin Nutr. 1981 Sep;34(9):1849-52. Pubmed: 6269418 Link_out
  5. Baig MM, Cerda JJ: Pectin: its interaction with serum lipoproteins. Am J Clin Nutr. 1981 Jan;34(1):50-3. Pubmed: 7446458 Link_out
  6. Lairon D, Lafont H, Vigne JL, Nalbone G, Leonardi J, Hauton JC: Effects of dietary fibers and cholestyramine on the activity of pancreatic lipase in vitro. Am J Clin Nutr. 1985 Oct;42(4):629-38. Pubmed: 2996326 Link_out
  7. Miettinen TA, Tarpila S: Effect of pectin on serum cholesterol, fecal bile acids and biliary lipids in normolipidemic and hyperlipidemic individuals. Clin Chim Acta. 1977 Sep 1;79(2):471-7. Pubmed: 890983 Link_out
  8. Bosaeus I, Carlsson NG, Sandberg AS, Andersson H: Effect of wheat bran and pectin on bile acid and cholesterol excretion in ileostomy patients. Hum Nutr Clin Nutr. 1986 Nov;40(6):429-40. Pubmed: 3025137 Link_out
  9. Fan TY, Feng QQ, Jia CR, Fan Q, Li CA, Bai XL: Protective effect of Weikang decoction and partial ingredients on model rat with gastric mucosa ulcer. World J Gastroenterol. 2005 Feb 28;11(8):1204-9. Pubmed: 15754406 Link_out
  10. Levy MC, Edwards-Levy F: Coating alginate beads with cross-linked biopolymers: a novel method based on a transacylation reaction. J Microencapsul. 1996 Mar-Apr;13(2):169-83. Pubmed: 8999122 Link_out
  11. Veldman FJ, Nair CH, Vorster HH, Vermaak WJ, Jerling JC, Oosthuizen W, Venter CS: Possible mechanisms through which dietary pectin influences fibrin network architecture in hypercholesterolaemic subjects. Thromb Res. 1999 Mar 15;93(6):253-64. Pubmed: 10093966 Link_out
  12. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. Pubmed: 19212411 Link_out
Enzymes
Name: UDP-glucuronosyltransferase 2B4
Reactions: Not Available
Gene Name: UGT2B4
Uniprot ID: P06133 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: UDP-glucuronosyltransferase 1-4
Reactions: Not Available
Gene Name: UGT1A4
Uniprot ID: P22310 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: UDP-glucuronosyltransferase 2B7
Reactions: Not Available
Gene Name: UGT2B7
Uniprot ID: P16662 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: UDP-glucuronosyltransferase 1-1
Reactions: Not Available
Gene Name: UGT1A1
Uniprot ID: P22309 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: UDP-glucuronosyltransferase 1-9
Reactions: Not Available
Gene Name: UGT1A9
Uniprot ID: O60656 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: UDP-glucuronosyltransferase 1-6
Reactions: Not Available
Gene Name: UGT1A6
Uniprot ID: P19224 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA