NP-MRD: Showing NP-Card for Gomphidic acid (NP0047671)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-03-17 20:44:00 UTC

Updated at

2022-03-17 20:44:00 UTC

NP-MRD ID

NP0047671

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Gomphidic acid

Description

Gomphidic acid, also known as gomphidate, belongs to the class of organic compounds known as pyrogallols and derivatives. Pyrogallols and derivatives are compounds containing a 1,2,3-trihydroxybenzene moiety. Gomphidic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Gomphidic acid has been detected, but not quantified in, mushrooms. This could make gomphidic acid a potential biomarker for the consumption of these foods.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05061307112D          

 27 29  0  0  0  0            999 V2000
   -0.2960   -0.1085    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6937   -0.4056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4675    0.6985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8653    0.4014    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3381   -0.6605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7796   -2.0195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9091   -0.6605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1665   -1.4675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2522    0.9534    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1227   -0.4056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5642   -1.7646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7376   -1.4675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7358   -0.9576    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
    0.0470   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3507   -2.0195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4237    1.7604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2942    0.4014    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1773   -2.3166    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5204   -0.7027    0.0000 O   0  0  0  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
   -1.1792   -2.8265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1353   -1.7646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    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
  7  1  2  0  0  0  0
  7  2  1  0  0  0  0
  8  5  2  0  0  0  0
  8  6  1  0  0  0  0
  9  3  2  0  0  0  0
  9  4  1  0  0  0  0
 10  5  1  0  0  0  0
 11  6  2  0  0  0  0
 12  8  1  0  0  0  0
 13  7  1  0  0  0  0
 14 10  2  0  0  0  0
 14 11  1  0  0  0  0
 15 12  2  0  0  0  0
 16 13  2  0  0  0  0
 16 15  1  0  0  0  0
 17 13  1  0  0  0  0
 18 12  1  0  0  0  0
 19  9  1  0  0  0  0
 20 10  1  0  0  0  0
 21 11  1  0  0  0  0
 22 14  1  0  0  0  0
 23 15  1  0  0  0  0
 24 17  2  0  0  0  0
 25 17  1  0  0  0  0
 26 18  2  0  0  0  0
 27 16  1  0  0  0  0
 27 18  1  0  0  0  0
M  END


  Mrv0541 05061307112D          

 27 29  0  0  0  0            999 V2000
   -0.2960   -0.1085    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6937   -0.4056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4675    0.6985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8653    0.4014    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3381   -0.6605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7796   -2.0195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9091   -0.6605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1665   -1.4675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2522    0.9534    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1227   -0.4056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5642   -1.7646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7376   -1.4675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7358   -0.9576    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
    0.0470   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3507   -2.0195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4237    1.7604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2942    0.4014    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1773   -2.3166    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5204   -0.7027    0.0000 O   0  0  0  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
   -1.1792   -2.8265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1353   -1.7646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    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
  7  1  2  0  0  0  0
  7  2  1  0  0  0  0
  8  5  2  0  0  0  0
  8  6  1  0  0  0  0
  9  3  2  0  0  0  0
  9  4  1  0  0  0  0
 10  5  1  0  0  0  0
 11  6  2  0  0  0  0
 12  8  1  0  0  0  0
 13  7  1  0  0  0  0
 14 10  2  0  0  0  0
 14 11  1  0  0  0  0
 15 12  2  0  0  0  0
 16 13  2  0  0  0  0
 16 15  1  0  0  0  0
 17 13  1  0  0  0  0
 18 12  1  0  0  0  0
 19  9  1  0  0  0  0
 20 10  1  0  0  0  0
 21 11  1  0  0  0  0
 22 14  1  0  0  0  0
 23 15  1  0  0  0  0
 24 17  2  0  0  0  0
 25 17  1  0  0  0  0
 26 18  2  0  0  0  0
 27 16  1  0  0  0  0
 27 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0047671

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)C(=C1/OC(=O)C(=C1O)C1=CC(O)=C(O)C(O)=C1)\C1=CC=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C18H12O9/c19-9-3-1-7(2-4-9)13(17(24)25)16-15(23)12(18(26)27-16)8-5-10(20)14(22)11(21)6-8/h1-6,19-23H,(H,24,25)/b16-13-

> <INCHI_KEY>
XLCYRDAATIMMJG-SSZFMOIBSA-N

> <FORMULA>
C18H12O9

> <MOLECULAR_WEIGHT>
372.2825

> <EXACT_MASS>
372.048131982

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
34.659470211942796

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-[(2Z)-3-hydroxy-5-oxo-4-(3,4,5-trihydroxyphenyl)-2,5-dihydrofuran-2-ylidene]-2-(4-hydroxyphenyl)acetic acid

> <ALOGPS_LOGP>
2.18

> <JCHEM_LOGP>
1.6340271916666664

> <ALOGPS_LOGS>
-3.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.2162650535591055

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.350163099938565

> <JCHEM_PKA_STRONGEST_BASIC>
-6.0127105173820015

> <JCHEM_POLAR_SURFACE_AREA>
164.74999999999997

> <JCHEM_REFRACTIVITY>
92.04579999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.26e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2Z)-3-hydroxy-5-oxo-4-(3,4,5-trihydroxyphenyl)furan-2-ylidene](4-hydroxyphenyl)acetic 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      -0.553  -0.203   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.162  -0.757   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.873   1.304   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.482   0.749   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.364  -1.233   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.189  -3.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.697  -1.233   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.044  -2.739   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.337   1.780   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.829  -0.757   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.653  -3.294   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.580  -3.215   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.377  -2.739   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.973  -1.788   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.088  -3.215   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.521  -3.770   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.104  -4.680   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -2.658   3.286   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       6.149   0.749   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       7.798  -4.324   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       8.438  -1.312   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -2.201  -5.276   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      -3.986  -3.294   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       3.009  -5.926   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       0.564  -4.680   0.000  0.00  0.00           O+0
CONECT    1    3    7                                                       
CONECT    2    4    7                                                       
CONECT    3    1    9                                                       
CONECT    4    2    9                                                       
CONECT    5    8   10                                                       
CONECT    6    8   11                                                       
CONECT    7    1    2   13                                                  
CONECT    8    5    6   12                                                  
CONECT    9    3    4   19                                                  
CONECT   10    5   14   20                                                  
CONECT   11    6   14   21                                                  
CONECT   12    8   15   18                                                  
CONECT   13    7   16   17                                                  
CONECT   14   10   11   22                                                  
CONECT   15   12   16   23                                                  
CONECT   16   13   15   27                                                  
CONECT   17   13   24   25                                                  
CONECT   18   12   26   27                                                  
CONECT   19    9                                                            
CONECT   20   10                                                            
CONECT   21   11                                                            
CONECT   22   14                                                            
CONECT   23   15                                                            
CONECT   24   17                                                            
CONECT   25   17                                                            
CONECT   26   18                                                            
CONECT   27   16   18                                                       
MASTER        0    0    0    0    0    0    0    0   27    0   58    0
END

View in JSmol

Synonyms

Value	Source
Gomphidate	Generator
4-Hydroxy-a-[3-hydroxy-5-oxo-4-(3,4,5-trihydroxyphenyl)-2(5H)-furanylidene]benzeneacetic acid, 9ci	HMDB
2-[(2Z)-3-Hydroxy-5-oxo-4-(3,4,5-trihydroxyphenyl)-2,5-dihydrofuran-2-ylidene]-2-(4-hydroxyphenyl)acetate	Generator

Chemical Formula

C₁₈H₁₂O₉

Average Mass

372.2825 Da

Monoisotopic Mass

372.04813 Da

IUPAC Name

2-[(2Z)-3-hydroxy-5-oxo-4-(3,4,5-trihydroxyphenyl)-2,5-dihydrofuran-2-ylidene]-2-(4-hydroxyphenyl)acetic acid

Traditional Name

[(2Z)-3-hydroxy-5-oxo-4-(3,4,5-trihydroxyphenyl)furan-2-ylidene](4-hydroxyphenyl)acetic acid

CAS Registry Number

25328-77-2

SMILES

OC(=O)C(=C1/OC(=O)C(=C1O)C1=CC(O)=C(O)C(O)=C1)\C1=CC=C(O)C=C1

InChI Identifier

InChI=1S/C18H12O9/c19-9-3-1-7(2-4-9)13(17(24)25)16-15(23)12(18(26)27-16)8-5-10(20)14(22)11(21)6-8/h1-6,19-23H,(H,24,25)/b16-13-

InChI Key

XLCYRDAATIMMJG-SSZFMOIBSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Agaricus bisporus	FooDB	Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Pleurotus ostreatus	FooDB	Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrogallols and derivatives. Pyrogallols and derivatives are compounds containing a 1,2,3-trihydroxybenzene moiety.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Phenols

Sub Class

Benzenetriols and derivatives

Direct Parent

Pyrogallols and derivatives

Alternative Parents

Substituents

Pyrogallol derivative
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Monocyclic benzene moiety
2-furanone
Dicarboxylic acid or derivatives
Dihydrofuran
Vinylogous acid
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Enol ester
Carboxylic acid ester
Lactone
Carboxylic acid derivative
Carboxylic acid
Oxacycle
Organoheterocyclic compound
Polyol
Enol
Organic oxygen compound
Organic oxide
Carbonyl group
Hydrocarbon derivative
Organooxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic 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	2.18	ALOGPS
logP	1.63	ChemAxon
logS	-3.5	ALOGPS
pKa (Strongest Acidic)	2.35	ChemAxon
pKa (Strongest Basic)	-6	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	164.75 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	92.05 m³·mol⁻¹	ChemAxon
Polarizability	34.66 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0033542

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB011604

KNApSAcK ID

Not Available

Chemspider ID

30777019

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

131751453

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Gomphidic acid (NP0047671)

MOL for NP0047671 (Gomphidic acid)

3D MOL for NP0047671 (Gomphidic acid)

3D SDF for NP0047671 (Gomphidic acid)

3D-SDF for NP0047671 (Gomphidic acid)

PDB for NP0047671 (Gomphidic acid)

3D PDB for NP0047671 (Gomphidic acid)

SMILES for NP0047671 (Gomphidic acid)

INCHI for NP0047671 (Gomphidic acid)

Structure for NP0047671 (Gomphidic acid)

3D Structure for NP0047671 (Gomphidic acid)