MiMeDB: Showing metabocard for Pectic acid (MMDBc0030374)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 00:05:45 UTC

Update Date

2024-04-30 19:46:11 UTC

Metabolite ID

MMDBc0030374

Metabolite Identification

Common Name

Pectic acid

Description

Pectic acid is also known as polygalacturonic acid. (Wikipedia ) In E. coli, pectic acid can be produced from pectin in a reaction catalyzed by pectinesterase (EC 3.1.1.11). (KEGG)

Structure

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


  Mrv0541 02231216592D          

 13 13  0  0  0  0            999 V2000
   -0.4391    0.3808    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4391   -0.4460    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2778    0.7926    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1562    0.7959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2778   -0.8542    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1493   -0.8577    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9880    0.3808    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8664    0.3842    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1527    1.6159    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9880   -0.4460    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2778   -1.6776    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7016    0.7891    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6982   -0.8577    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  1  0  0  0
  2  5  1  0  0  0  0
  2  6  1  1  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  4  9  2  0  0  0  0
  5 10  1  0  0  0  0
  5 11  1  1  0  0  0
  7 12  1  6  0  0  0
 10 13  1  6  0  0  0
  7 10  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030374

> <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-BKBMJHBISA-N

> <FORMULA>
C6H10O7

> <MOLECULAR_WEIGHT>
194.1394

> <EXACT_MASS>
194.042652674

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
16.26778435795166

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5R,6S)-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>
127.45

> <JCHEM_REFRACTIVITY>
35.7908

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.95e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
α-D-galacturonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      -0.820   0.711   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.820  -0.833   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.519   1.480   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -2.158   1.486   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.519  -1.595   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -2.145  -1.601   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       1.844   0.711   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -3.484   0.717   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -2.152   3.016   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       1.844  -0.833   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.519  -3.132   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       3.176   1.473   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       3.170  -1.601   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7                                                       
CONECT    4    1    8    9                                                  
CONECT    5    2   10   11                                                  
CONECT    6    2                                                            
CONECT    7    3   12   10                                                  
CONECT    8    4                                                            
CONECT    9    4                                                            
CONECT   10    5   13    7                                                  
CONECT   11    5                                                            
CONECT   12    7                                                            
CONECT   13   10                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

Synonyms

Value	Source
Pectate	Generator
a-D-Galacturonate	HMDB
a-D-Galacturonic acid	HMDB
alpha-D-Galacturonate	HMDB
Α-D-galacturonate	HMDB
Α-D-galacturonic acid	HMDB
alpha-delta-Galactopyranuronic acid	HMDB
alpha-delta-Galacturonic acid	HMDB
alpha-delta-Polygalacturonic acid	HMDB
Calcium pectate	HMDB
Calcium polygalacturonate	HMDB
D-Galacturonan	HMDB
D-Galacturonate	HMDB
delta-Galacturonan	HMDB
delta-Galacturonate	HMDB
delta-Galacturonic acid	HMDB
Galacturonan	HMDB
Galacturonate	HMDB
Poly(1,4-alpha-D-galacturonate)	HMDB
Poly(1,4-alpha-delta-galacturonate)	HMDB
Polygalacturonic acid	HMDB
Sodium pectate	HMDB
Sulfated polygalacturonic acid	HMDB
Polygalacturonic acid, aluminum salt	HMDB
Polygalacturonic acid, homopolymer sodium salt	HMDB
Polygalacturonic acid, sulfated	HMDB
Polygalacturonic acid, calcium salt	HMDB
Polygalacturonic acid homopolymer	HMDB
Homogalacturonan	HMDB
Polygalacturonic acid, homopolymer (D)-isomer	HMDB
Sodium polygalacturonate	HMDB
Pectic acid	MeSH

Molecular Formula

C₆H₁₀O₇

Average Mass

194.1394

Monoisotopic Mass

194.042652674

IUPAC Name

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

Traditional Name

α-D-galacturonic acid

CAS Registry Number

Not Available

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-BKBMJHBISA-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:33885 )

Functional Ontology

Not Available

Physical Properties

State

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	16.27 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a6s-5900000000-4145d7dbe91803d8047f	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (5 TMS) - 70eV, Positive	splash10-000l-6242950000-7b610ed98440b47c2a32	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004j-0900000000-6a9a5aa935dacf9a0639	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004j-1900000000-089cf378755226bdb184	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052r-9500000000-e57843f461582ce2d542	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0007-1900000000-ff3896e4e300eaf408f4	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0035-4900000000-78473708a7867d8c7fc3	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9200000000-47b1621c98981a6c3318	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-3900000000-64f3d0eb26f7bc8ca624	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a73-9300000000-329488f791f643b1c308	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9000000000-474e82a5911096bc3b39	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-0900000000-2877a7e6d3ecd32cf172	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000b-7900000000-d748e59637b495442c9e	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03dl-9100000000-40ac961f184de816ed86	2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Feces

Tissue Locations

Not Available

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

Not Available

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	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	25037050
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	29808030

External Links

HMDB ID

HMDB0003363

DrugBank ID

DB03511

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB021453

KNApSAcK ID

Not Available

Chemspider ID

393411

KEGG Compound ID

C00470

BioCyc ID

PECTATE

BiGG ID

Not Available

Wikipedia Link

Pectic acid

METLIN ID

6904

PubChem Compound

445929

PDB ID

Not Available

ChEBI ID

33885

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Serban D, Rordorf-Adam C: Binding characteristics of human serum amyloid P component. Scand J Immunol. 1987 Mar;25(3):275-81. doi: 10.1111/j.1365-3083.1987.tb01073.x. [PubMed:3105045 ]
Nakajima N, Ishihara K, Matsuura Y: Dietary-fiber-degrading enzymes from a human intestinal Clostridium and their application to oligosaccharide production from nonstarchy polysaccharides using immobilized cells. Appl Microbiol Biotechnol. 2002 Jul;59(2-3):182-9. doi: 10.1007/s00253-002-1015-7. Epub 2002 May 3. [PubMed:12111144 ]

Showing metabocard for Pectic acid (MMDBc0030374)

MOL for #<Metabolite:0x00007fececf1acd0>

3D MOL for #<Metabolite:0x00007fececf1acd0>

3D SDF for #<Metabolite:0x00007fececf1acd0>

3D-SDF for #<Metabolite:0x00007fececf1acd0>

PDB for #<Metabolite:0x00007fececf1acd0>

3D PDB for #<Metabolite:0x00007fececf1acd0>

SMILES for #<Metabolite:0x00007fececf1acd0>

INCHI for #<Metabolite:0x00007fececf1acd0>

Structure for #<Metabolite:0x00007fececf1acd0>

3D Structure for #<Metabolite:0x00007fececf1acd0>