MiMeDB: Showing metabocard for Pectin (MMDBc0000239)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-10-27 23:40:56 UTC

Update Date

2024-04-30 19:31:39 UTC

Metabolite ID

MMDBc0000239

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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv1652303202019292D          

 13 13  0  0  1  0            999 V2000
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  2  9  1  0  0  0  0
  9 10  1  1  0  0  0
  4 11  1  6  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000239

> <DATABASE_NAME>
MIME

> <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

> <FORMULA>
C6H10O7

> <MOLECULAR_WEIGHT>
194.1394

> <EXACT_MASS>
194.042652674

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
16.369534945317536

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5R,6R)-3,4,5,6-tetrahydroxyoxane-2-carboxylic acid

> <ALOGPS_LOGP>
-2.30

> <JCHEM_LOGP>
-2.61226468

> <ALOGPS_LOGS>
0.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.309229286068723

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.207791058651709

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6863365702254773

> <JCHEM_POLAR_SURFACE_AREA>
127.45000000000002

> <JCHEM_REFRACTIVITY>
35.7908

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.95e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
β-D-galactopyranuronic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAR-20         0                                  
HETATM    1  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   11                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7    2   10                                                  
CONECT   10    9                                                            
CONECT   11    4   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

Synonyms

Value	Source
(+)-Xylose	HMDB
2,3,4,5-Tetrahydroxypentanal	HMDB
D-Lyxose	HMDB
DL-Xylose	HMDB
L(+)-Xylose	HMDB
L-Lyxose	HMDB
Lyxose	HMDB
Pectin sugar	HMDB
Pectinose	HMDB
Pentose	HMDB
Trobicin	HMDB
Pectinic acid	HMDB
Calcium pectinate	HMDB
Methoxy pectin	HMDB
Methoxylpectin	HMDB
Methoxypectin	HMDB
Zinc pectinate	HMDB
Galacturonate	HMDB
b-D-Galacturonate	HMDB
b-D-Galacturonic acid	HMDB
beta-D-Galacturonate	HMDB
Β-D-galacturonate	HMDB
Β-D-galacturonic acid	HMDB
Pectin	MeSH
b-D-Galactopyranuronate	Generator
b-D-Galactopyranuronic acid	Generator
beta-D-Galactopyranuronate	Generator
Β-D-galactopyranuronate	Generator
Β-D-galactopyranuronic acid	Generator

Molecular Formula

C₆H₁₀O₇

Average Mass

194.1394

Monoisotopic Mass

194.042652674

IUPAC Name

(2S,3R,4S,5R,6R)-3,4,5,6-tetrahydroxyoxane-2-carboxylic acid

Traditional Name

β-D-galactopyranuronic 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

Description

Belongs to the class of organic compounds known as glucuronic acid derivatives. Glucuronic acid derivatives are compounds containing a glucuronic acid moiety (or a derivative), which consists of a glucose moiety with the C6 carbon oxidized to a carboxylic acid.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Glucuronic acid derivatives

Alternative Parents

Substituents

Glucuronic acid or derivatives
Beta-hydroxy acid
Hydroxy acid
Pyran
Monosaccharide
Oxane
Hemiacetal
Secondary alcohol
Carboxylic acid derivative
Carboxylic acid
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Polyol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

D-galactopyranuronic acid (CHEBI:47954 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	295 g/L	ALOGPS
logP	-2.3	ALOGPS
logP	-2.6	ChemAxon
logS	0.18	ALOGPS
pKa (Strongest Acidic)	3.21	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	127.45 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	35.79 m³·mol⁻¹	ChemAxon
Polarizability	16.37 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Extracellular
Lysosome

Biospecimen Locations

Adipose Tissue
Bladder
Epidermis
Feces
Fibroblasts
Intestine
Kidney
Neuron
Placenta
Platelet
Prostate
Skeletal Muscle
Spleen
Testis
Urine

Tissue Locations

Adipose Tissue
Bladder
Epidermis
Fibroblasts
Intestine
Kidney
Neuron
Placenta
Platelet
Prostate
Skeletal Muscle
Spleen
Testis

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0192118	UDP-glucuronosyltransferase 2B4	Enzyme	P06133	Homo sapiens
MMDBp0192135	UDP-glucuronosyltransferase 1-4	Enzyme	P22310	Homo sapiens
MMDBp0192137	UDP-glucuronosyltransferase 2B7	Enzyme	P16662	Homo sapiens
MMDBp0192140	UDP-glucuronosyltransferase 1-1	Enzyme	P22309	Homo sapiens
MMDBp0192141	UDP-glucuronosyltransferase 1-9	Enzyme	O60656	Homo sapiens
MMDBp0192146	UDP-glucuronosyltransferase 1-6	Enzyme	P19224	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Bacteroidetes	16	Human feces; Human ; Human urine; Human stool; Human saliva	Microbial culture; Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	36	Human feces; Human ; Human saliva; Human subgingival plaque; Human stool	Microbial culture; Metabolic reconstruction
Bacteria/Eubacteria	Spirochaetes	1		Microbial culture
Bacteria/Eubacteria	Actinobacteria	12	Human feces; Human ; Human mucosa; Human supragingival plaque; Human subgingival plaque; Human saliva; Human stool	Microbial culture; Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	1		Microbial culture
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Food Exposures

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified								HMDB
Human Urine	Detected and Quantified	5.26	4.0	7.0	umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	Geigy Scientific Tables, 8th Rev edition, pp. 130. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp. Basel, Switzerland c1981-1992.
Human Adipose tissue	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Bladder	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Epidermis	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Fibroblasts	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Intestine	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Kidney	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Neuron	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Placenta	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Platelet	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Prostate	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Skeletal muscle	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Spleen	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Testis	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Urine	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	28157703

External Links

HMDB ID

HMDB0003402

DrugBank ID

DB03652

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023162

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

47954

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

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. doi: 10.1016/0009-8981(77)90444-2. [PubMed:890983 ]
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. doi: 10.1093/ajcn/42.4.629. [PubMed:2996326 ]
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 ]
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. doi: 10.1093/ajcn/34.9.1849. [PubMed:6269418 ]
Fleming SE, Marthinsen D, Kuhnlein H: Colonic function and fermentation in men consuming high fiber diets. J Nutr. 1983 Dec;113(12):2535-44. doi: 10.1093/jn/113.12.2535. [PubMed:6317826 ]
Baig MM, Cerda JJ: Pectin: its interaction with serum lipoproteins. Am J Clin Nutr. 1981 Jan;34(1):50-3. doi: 10.1093/ajcn/34.1.50. [PubMed:7446458 ]
Lewinska D, Rosinski S, Piatkiewicz W: A new pectin-based material for selective LDL-cholesterol removal. Artif Organs. 1994 Mar;18(3):217-22. doi: 10.1111/j.1525-1594.1994.tb02179.x. [PubMed:8185488 ]
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. doi: 10.3109/02652049609052905. [PubMed:8999122 ]
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. doi: 10.1016/s0049-3848(98)00170-4. [PubMed:10093966 ]
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. doi: 10.1177/014860719902300518. [PubMed:10483900 ]
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. doi: 10.3748/wjg.v11.i8.1204. [PubMed:15754406 ]
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. doi: 10.1038/nature07762. [PubMed:19212411 ]

Showing metabocard for Pectin (MMDBc0000239)

MOL for #<Metabolite:0x00007f9258076c68>

3D MOL for #<Metabolite:0x00007f9258076c68>

3D SDF for #<Metabolite:0x00007f9258076c68>

3D-SDF for #<Metabolite:0x00007f9258076c68>

PDB for #<Metabolite:0x00007f9258076c68>

3D PDB for #<Metabolite:0x00007f9258076c68>

SMILES for #<Metabolite:0x00007f9258076c68>

INCHI for #<Metabolite:0x00007f9258076c68>

Structure for #<Metabolite:0x00007f9258076c68>

3D Structure for #<Metabolite:0x00007f9258076c68>