NP-MRD: Showing NP-Card for Lepidimoic acid (NP0049788)

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Record Information

Version

2.0

Created at

2022-03-17 21:18:08 UTC

Updated at

2022-03-17 21:18:08 UTC

NP-MRD ID

NP0049788

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Lepidimoic acid

Description

Lepidimoic acid, also known as lepidimoate, belongs to the class of organic compounds known as disaccharides. Disaccharides are compounds containing two carbohydrate moieties linked to each to each other through a glycosidic bond, no set of three or more glycosidically linked carbohydrate units. Lepidimoic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Lepidimoic acid has been detected, but not quantified in, brassicas and garden cress. Lepidimoic acid is found in Arabidopsis thaliana and Hibiscus exculentus. Lepidimoic acid was first documented in 2001 (PMID: 11261583). This could make lepidimoic acid a potential biomarker for the consumption of these foods.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05061312232D          

 22 23  0  0  0  0            999 V2000
    7.4064   -2.9062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2630    1.6312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4064   -2.0812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9775    2.0438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2630    0.8062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1209   -1.6687    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6920    1.6313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1209   -0.8437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4064   -0.4312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5485    0.3937    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6920   -0.8437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6920    0.8063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9775    2.8688    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.8354   -2.0812    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4064    2.0438    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.8354   -0.4312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8341    0.8062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5485   -0.4313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9775   -0.4312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6920   -1.6687    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9775    0.3937    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4064    0.3938    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  2  2  0  0  0  0
  6  3  1  0  0  0  0
  7  4  1  0  0  0  0
  8  6  1  0  0  0  0
  9  8  1  0  0  0  0
 10  5  1  0  0  0  0
 11  9  1  0  0  0  0
 12  7  1  0  0  0  0
 13  4  1  0  0  0  0
 14  6  1  0  0  0  0
 15  7  1  0  0  0  0
 16  8  1  0  0  0  0
 17 10  2  0  0  0  0
 18 10  1  0  0  0  0
 19 11  1  0  0  0  0
 20  3  1  0  0  0  0
 20 11  1  0  0  0  0
 21  5  1  0  0  0  0
 21 12  1  0  0  0  0
 22  9  1  0  0  0  0
 22 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0049788

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1OC(O)C(OC2OC(=CC(O)C2O)C(O)=O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C12H18O10/c1-3-6(14)8(16)9(11(19)20-3)22-12-7(15)4(13)2-5(21-12)10(17)18/h2-4,6-9,11-16,19H,1H3,(H,17,18)

> <INCHI_KEY>
PBUKNNGDHZLXKG-UHFFFAOYSA-N

> <FORMULA>
C12H18O10

> <MOLECULAR_WEIGHT>
322.2653

> <EXACT_MASS>
322.089996796

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
29.235303420316658

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,4-dihydroxy-2-[(2,4,5-trihydroxy-6-methyloxan-3-yl)oxy]-3,4-dihydro-2H-pyran-6-carboxylic acid

> <ALOGPS_LOGP>
-2.20

> <JCHEM_LOGP>
-2.5972615973333326

> <ALOGPS_LOGS>
-0.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.285758919082857

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1692421120405387

> <JCHEM_PKA_STRONGEST_BASIC>
-3.4544885868113298

> <JCHEM_POLAR_SURFACE_AREA>
166.14

> <JCHEM_REFRACTIVITY>
67.02140000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.10e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4,5-dihydroxy-6-[(2,4,5-trihydroxy-6-methyloxan-3-yl)oxy]-5,6-dihydro-4H-pyran-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0      13.825  -5.425   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.824   3.045   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      13.825  -3.885   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      11.158   3.815   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.824   1.505   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      15.159  -3.115   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.492   3.045   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      15.159  -1.575   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      13.825  -0.805   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.491   0.735   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      12.492  -1.575   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.492   1.505   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      11.158   5.355   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      16.493  -3.885   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      13.825   3.815   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      16.493  -0.805   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       7.157   1.505   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       8.491  -0.805   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      11.158  -0.805   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      12.492  -3.115   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      11.158   0.735   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      13.825   0.735   0.000  0.00  0.00           O+0
CONECT    1    3                                                            
CONECT    2    4    5                                                       
CONECT    3    1    6   20                                                  
CONECT    4    2    7   13                                                  
CONECT    5    2   10   21                                                  
CONECT    6    3    8   14                                                  
CONECT    7    4   12   15                                                  
CONECT    8    6    9   16                                                  
CONECT    9    8   11   22                                                  
CONECT   10    5   17   18                                                  
CONECT   11    9   19   20                                                  
CONECT   12    7   21   22                                                  
CONECT   13    4                                                            
CONECT   14    6                                                            
CONECT   15    7                                                            
CONECT   16    8                                                            
CONECT   17   10                                                            
CONECT   18   10                                                            
CONECT   19   11                                                            
CONECT   20    3   11                                                       
CONECT   21    5   12                                                       
CONECT   22    9   12                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   46    0
END

View in JSmol

Synonyms

Value	Source
Lepidimoate	Generator
1-Methyl-3-phenyl-5-(3-propoxyphenyl)pyridin-4-one	HMDB
2-O-L-Ramnopyranosyl-4-deoxy-alpha-L-threo-hex-4-enopyranosiduronoic acid	HMDB
6-Deoxy-2-O-(4-deoxy-b-L-threo-hex-4-enopyranuronosyl)-L-mannose, 9ci	HMDB
Lepidimoide	HMDB
2-O-L-Rhamnopyranosyl-4-deoxy-alpha-L-threo-hex-4-enopyranosiduronate	MeSH
3,4-Dihydroxy-2-[(2,4,5-trihydroxy-6-methyloxan-3-yl)oxy]-3,4-dihydro-2H-pyran-6-carboxylate	Generator

Chemical Formula

C₁₂H₁₈O₁₀

Average Mass

322.2653 Da

Monoisotopic Mass

322.09000 Da

IUPAC Name

3,4-dihydroxy-2-[(2,4,5-trihydroxy-6-methyloxan-3-yl)oxy]-3,4-dihydro-2H-pyran-6-carboxylic acid

Traditional Name

4,5-dihydroxy-6-[(2,4,5-trihydroxy-6-methyloxan-3-yl)oxy]-5,6-dihydro-4H-pyran-2-carboxylic acid

CAS Registry Number

157676-09-0

SMILES

CC1OC(O)C(OC2OC(=CC(O)C2O)C(O)=O)C(O)C1O

InChI Identifier

InChI=1S/C12H18O10/c1-3-6(14)8(16)9(11(19)20-3)22-12-7(15)4(13)2-5(21-12)10(17)18/h2-4,6-9,11-16,19H,1H3,(H,17,18)

InChI Key

PBUKNNGDHZLXKG-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Arabidopsis thaliana	Plant	KNApSAcK
Hibiscus exculentus	Plant	KNApSAcK
Lepidium sativum	FooDB	KNAPSACK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as disaccharides. Disaccharides are compounds containing two carbohydrate moieties linked to each to each other through a glycosidic bond, no set of three or more glycosidically linked carbohydrate units.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Disaccharides

Alternative Parents

Substituents

Disaccharide
Oxane
Hemiacetal
Secondary alcohol
Acetal
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Oxacycle
Organoheterocyclic compound
Polyol
Hydrocarbon derivative
Carbonyl group
Alcohol
Organic oxide
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

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
logP	-2.2	ALOGPS
logP	-2.6	ChemAxon
logS	-0.47	ALOGPS
pKa (Strongest Acidic)	3.17	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	166.14 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	67.02 m³·mol⁻¹	ChemAxon
Polarizability	29.24 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0041096

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB020978

KNApSAcK ID

C00007670

Chemspider ID

3677082

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

4479101

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Kato-Noguchi H, Yamada K, Hasegawa K: Lepidimoic acid increases fructose 2,6-bisphosphate in Amaranthus seedlings. Phytochemistry. 2001 Mar;56(5):499-503. doi: 10.1016/s0031-9422(00)00389-7. [PubMed:11261583 ]

Showing NP-Card for Lepidimoic acid (NP0049788)

MOL for NP0049788 (Lepidimoic acid)

3D MOL for NP0049788 (Lepidimoic acid)

3D SDF for NP0049788 (Lepidimoic acid)

3D-SDF for NP0049788 (Lepidimoic acid)

PDB for NP0049788 (Lepidimoic acid)

3D PDB for NP0049788 (Lepidimoic acid)

SMILES for NP0049788 (Lepidimoic acid)

INCHI for NP0049788 (Lepidimoic acid)

Structure for NP0049788 (Lepidimoic acid)

3D Structure for NP0049788 (Lepidimoic acid)