NP-MRD: Showing NP-Card for 2,3-dihydroxy-2-[(4-hydroxyphenyl)methyl]butanedioic acid (NP0306525)

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Record Information

Version

2.0

Created at

2022-09-10 23:03:01 UTC

Updated at

2022-09-10 23:03:01 UTC

NP-MRD ID

NP0306525

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2,3-dihydroxy-2-[(4-hydroxyphenyl)methyl]butanedioic acid

Description

(2R,3S)-Piscidic acid, also known as (2R,3S)-piscidate, belongs to the class of organic compounds known as phenylpropanoic acids. Phenylpropanoic acids are compounds with a structure containing a benzene ring conjugated to a propanoic acid (2R,3S)-Piscidic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, (2R,3S)-Piscidic acid has been detected, but not quantified in, fruits and green vegetables. 2,3-dihydroxy-2-[(4-hydroxyphenyl)methyl]butanedioic acid is found in Actaea simplex, Narcissus poeticus, Piscidia piscipula and Sophora alopecuroides. This could make (2R,3S)-piscidic acid a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 30 30  0  0  0  0  0  0  0  0999 V2000
   -3.5302    0.4786    1.2783 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2536    0.6485    0.0715 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5445    1.9201   -0.4478 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6622   -0.4141   -0.7506 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5545    0.0824   -2.0739 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2203   -0.7633   -0.3510 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8409   -1.7123   -1.3253 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4194    0.4877   -0.4567 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0041    0.3311   -0.1061 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9316   -0.0098   -1.0861 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2655   -0.1590   -0.7765 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7453    0.0197    0.5057 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0898   -0.1291    0.8262 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8405    0.3573    1.4875 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4926    0.5073    1.1708 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2164   -1.4122    0.9605 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9653   -2.6696    1.0412 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4655   -0.7690    2.1557 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9535    2.7106   -0.3465 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2579   -1.3215   -0.7984 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6459    1.0669   -2.0824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0153   -1.3956   -2.2286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8603    1.2214    0.2652 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5391    0.8602   -1.5082 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6144   -0.1620   -2.1055 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0091   -0.4275   -1.5381 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7421    0.6316    0.7884 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2059    0.5006    2.5002 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7944    0.7748    1.9586 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7905   -1.2541    2.9720 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  4  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  4  6  1  0
  6  7  1  6
  6  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 12 14  1  0
 14 15  2  0
  6 16  1  0
 16 18  1  0
 16 17  2  0
 15  9  1  0
  5 21  1  0
  4 20  1  6
  3 19  1  0
  7 22  1  0
  8 23  1  0
  8 24  1  0
 10 25  1  0
 11 26  1  0
 13 27  1  0
 14 28  1  0
 15 29  1  0
 18 30  1  0
M  END


  Mrv0541 05061305312D          

 18 18  0  0  0  0            999 V2000
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   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
    0.7145   -0.4125    0.0000 C   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
    2.1434   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  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
    2.1434   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -3.0789    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914   -2.3645    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8414   -0.9355    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  2  0  0  0  0
  6  1  2  0  0  0  0
  6  2  1  0  0  0  0
  6  5  1  0  0  0  0
  7  3  2  0  0  0  0
  7  4  1  0  0  0  0
  9  8  1  0  0  0  0
 11  5  1  0  0  0  0
 11  8  1  0  0  0  0
 11 10  1  0  0  0  0
 12  7  1  0  0  0  0
 13  8  1  0  0  0  0
 14  9  2  0  0  0  0
 15  9  1  0  0  0  0
 16 10  2  0  0  0  0
 17 10  1  0  0  0  0
 18 11  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0306525

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(C(O)=O)C(O)(CC1=CC=C(O)C=C1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H12O7/c12-7-3-1-6(2-4-7)5-11(18,10(16)17)8(13)9(14)15/h1-4,8,12-13,18H,5H2,(H,14,15)(H,16,17)

> <INCHI_KEY>
TUODPMGCCJSJRH-UHFFFAOYSA-N

> <FORMULA>
C11H12O7

> <MOLECULAR_WEIGHT>
256.2088

> <EXACT_MASS>
256.058302738

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
22.848586188648415

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2,3-dihydroxy-2-[(4-hydroxyphenyl)methyl]butanedioic acid

> <ALOGPS_LOGP>
-0.02

> <JCHEM_LOGP>
-0.043272956666666834

> <ALOGPS_LOGS>
-1.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.70034013433595

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2074587835648773

> <JCHEM_PKA_STRONGEST_BASIC>
-4.398660262447797

> <JCHEM_POLAR_SURFACE_AREA>
135.29000000000002

> <JCHEM_REFRACTIVITY>
57.5266

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.99e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3-dihydroxy-2-[(4-hydroxyphenyl)methyl]butanedioic 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       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001  -3.850   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.897  -4.414   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       4.001  -5.390   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       6.668  -3.850   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       5.335  -1.540   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       2.667  -5.747   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.357  -4.414   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       3.437  -1.746   0.000  0.00  0.00           O+0
CONECT    1    3    6                                                       
CONECT    2    4    6                                                       
CONECT    3    1    7                                                       
CONECT    4    2    7                                                       
CONECT    5    6   11                                                       
CONECT    6    1    2    5                                                  
CONECT    7    3    4   12                                                  
CONECT    8    9   11   13                                                  
CONECT    9    8   14   15                                                  
CONECT   10   11   16   17                                                  
CONECT   11    5    8   10   18                                             
CONECT   12    7                                                            
CONECT   13    8                                                            
CONECT   14    9                                                            
CONECT   15    9                                                            
CONECT   16   10                                                            
CONECT   17   10                                                            
CONECT   18   11                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

View in JSmol

Synonyms

Value	Source
(2R,3S)-Piscidate	Generator
2,3-Dihydroxy-2-[(4-hydroxyphenyl)methyl]butanedioate	Generator
Piscidic acid, (S-(r,s))-isomer	MeSH
Piscidic acid	MeSH
(p-Hydroxybenzyl)tartaric acid	MeSH

Chemical Formula

C₁₁H₁₂O₇

Average Mass

256.2088 Da

Monoisotopic Mass

256.05830 Da

IUPAC Name

2,3-dihydroxy-2-[(4-hydroxyphenyl)methyl]butanedioic acid

Traditional Name

2,3-dihydroxy-2-[(4-hydroxyphenyl)methyl]butanedioic acid

CAS Registry Number

Not Available

SMILES

OC(C(O)=O)C(O)(CC1=CC=C(O)C=C1)C(O)=O

InChI Identifier

InChI=1S/C11H12O7/c12-7-3-1-6(2-4-7)5-11(18,10(16)17)8(13)9(14)15/h1-4,8,12-13,18H,5H2,(H,14,15)(H,16,17)

InChI Key

TUODPMGCCJSJRH-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Actaea simplex	LOTUS Database	35616633
Narcissus poeticus	LOTUS Database	35616633
Piscidia piscipula	LOTUS Database	35616633
Sophora alopecuroides	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenylpropanoic acids. Phenylpropanoic acids are compounds with a structure containing a benzene ring conjugated to a propanoic acid.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Phenylpropanoic acids

Sub Class

Not Available

Direct Parent

Phenylpropanoic acids

Alternative Parents

Substituents

3-phenylpropanoic-acid
1-hydroxy-2-unsubstituted benzenoid
Beta-hydroxy acid
Phenol
Alpha-hydroxy acid
Monocyclic benzene moiety
Dicarboxylic acid or derivatives
Hydroxy acid
Monosaccharide
Benzenoid
Tertiary alcohol
1,2-diol
Secondary alcohol
Carboxylic acid
Carboxylic acid derivative
Alcohol
Carbonyl group
Organooxygen compound
Organic oxide
Hydrocarbon derivative
Organic oxygen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic 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	-0.02	ALOGPS
logP	-0.043	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	3.21	ChemAxon
pKa (Strongest Basic)	-4.4	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	135.29 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	57.53 m³·mol⁻¹	ChemAxon
Polarizability	22.85 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0030809

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB002762

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

120693

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2,3-dihydroxy-2-[(4-hydroxyphenyl)methyl]butanedioic acid (NP0306525)

MOL for NP0306525 (2,3-dihydroxy-2-[(4-hydroxyphenyl)methyl]butanedioic acid)

3D MOL for NP0306525 (2,3-dihydroxy-2-[(4-hydroxyphenyl)methyl]butanedioic acid)

3D SDF for NP0306525 (2,3-dihydroxy-2-[(4-hydroxyphenyl)methyl]butanedioic acid)

3D-SDF for NP0306525 (2,3-dihydroxy-2-[(4-hydroxyphenyl)methyl]butanedioic acid)

PDB for NP0306525 (2,3-dihydroxy-2-[(4-hydroxyphenyl)methyl]butanedioic acid)

3D PDB for NP0306525 (2,3-dihydroxy-2-[(4-hydroxyphenyl)methyl]butanedioic acid)

SMILES for NP0306525 (2,3-dihydroxy-2-[(4-hydroxyphenyl)methyl]butanedioic acid)

INCHI for NP0306525 (2,3-dihydroxy-2-[(4-hydroxyphenyl)methyl]butanedioic acid)

Structure for NP0306525 (2,3-dihydroxy-2-[(4-hydroxyphenyl)methyl]butanedioic acid)

3D Structure for NP0306525 (2,3-dihydroxy-2-[(4-hydroxyphenyl)methyl]butanedioic acid)