NP-MRD: Showing NP-Card for Urolithin c 3-glucuronide (NP0334549)

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Record Information

Version

2.0

Created at

2024-09-10 00:08:20 UTC

Updated at

2024-09-10 00:08:20 UTC

NP-MRD ID

NP0334549

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Urolithin c 3-glucuronide

Description

NULL

Structure

MOL SDF PDB SMILES InChI


  Mrv1652310161916432D          

 35 38  0  0  1  0            999 V2000
   -1.1270   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3480   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1730    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9355    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3480    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1730   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5855    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0145   -1.0164    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.6020   -1.7309    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.6020   -0.3020    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7770   -1.7309    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3645   -2.4454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9355    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7770   -0.3020    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5855   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4105    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8395   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0145   -2.4454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0145    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5395   -2.4454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7770   -3.1599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3480    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3645    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3645   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4270   -1.7309    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1895   -2.4454    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1895    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1895   -1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9520   -0.3020    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  6  1  1  0  0  0  0
  6  3  2  0  0  0  0
  7  2  1  0  0  0  0
  8  4  2  0  0  0  0
  8  7  1  0  0  0  0
  9  5  2  0  0  0  0
  9  8  1  0  0  0  0
 10  4  1  0  0  0  0
 11  5  1  0  0  0  0
 11 10  2  0  0  0  0
 12  3  1  0  0  0  0
 12  7  2  0  0  0  0
 14 13  1  0  0  0  0
 15 13  1  0  0  0  0
 16 14  1  0  0  0  0
 16 17  1  1  0  0  0
 18  9  1  0  0  0  0
 19 15  1  0  0  0  0
 20 10  1  0  0  0  0
 21 11  1  0  0  0  0
 13 22  1  6  0  0  0
 14 23  1  1  0  0  0
 15 24  1  1  0  0  0
 25 17  2  0  0  0  0
 26 17  1  0  0  0  0
 27 18  2  0  0  0  0
 28  6  1  0  0  0  0
 19 28  1  6  0  0  0
 29 12  1  0  0  0  0
 29 18  1  0  0  0  0
 30 16  1  0  0  0  0
 30 19  1  0  0  0  0
 13 31  1  1  0  0  0
 14 32  1  6  0  0  0
 15 33  1  6  0  0  0
 16 34  1  1  0  0  0
 19 35  1  1  0  0  0
M  END


  Mrv1652310161916432D          

 35 38  0  0  1  0            999 V2000
   -1.1270   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3480   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1730    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9355    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3480    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1730   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5855    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0145   -1.0164    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.6020   -1.7309    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.6020   -0.3020    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7770   -1.7309    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3645   -2.4454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9355    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7770   -0.3020    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5855   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4105    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8395   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0145   -2.4454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0145    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5395   -2.4454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7770   -3.1599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3480    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3645    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3645   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4270   -1.7309    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1895   -2.4454    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1895    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1895   -1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9520   -0.3020    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  6  1  1  0  0  0  0
  6  3  2  0  0  0  0
  7  2  1  0  0  0  0
  8  4  2  0  0  0  0
  8  7  1  0  0  0  0
  9  5  2  0  0  0  0
  9  8  1  0  0  0  0
 10  4  1  0  0  0  0
 11  5  1  0  0  0  0
 11 10  2  0  0  0  0
 12  3  1  0  0  0  0
 12  7  2  0  0  0  0
 14 13  1  0  0  0  0
 15 13  1  0  0  0  0
 16 14  1  0  0  0  0
 16 17  1  1  0  0  0
 18  9  1  0  0  0  0
 19 15  1  0  0  0  0
 20 10  1  0  0  0  0
 21 11  1  0  0  0  0
 13 22  1  6  0  0  0
 14 23  1  1  0  0  0
 15 24  1  1  0  0  0
 25 17  2  0  0  0  0
 26 17  1  0  0  0  0
 27 18  2  0  0  0  0
 28  6  1  0  0  0  0
 19 28  1  6  0  0  0
 29 12  1  0  0  0  0
 29 18  1  0  0  0  0
 30 16  1  0  0  0  0
 30 19  1  0  0  0  0
 13 31  1  1  0  0  0
 14 32  1  6  0  0  0
 15 33  1  6  0  0  0
 16 34  1  1  0  0  0
 19 35  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0334549

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]1(OC2=CC3=C(C=C2)C2=CC(O)=C(O)C=C2C(=O)O3)O[C@]([H])(C(O)=O)[C@@]([H])(O)[C@]([H])(O)[C@@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C19H16O11/c20-10-4-8-7-2-1-6(3-12(7)29-18(27)9(8)5-11(10)21)28-19-15(24)13(22)14(23)16(30-19)17(25)26/h1-5,13-16,19-24H,(H,25,26)/t13-,14-,15+,16-,19+/m0/s1

> <INCHI_KEY>
DDAQYQCCOWZGDO-KSPMYQCISA-N

> <FORMULA>
C19H16O11

> <MOLECULAR_WEIGHT>
420.326

> <EXACT_MASS>
420.069261335

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
46

> <JCHEM_AVERAGE_POLARIZABILITY>
38.920434156855954

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S,3S,4S,5R,6S)-6-({8,9-dihydroxy-6-oxo-6H-benzo[c]chromen-3-yl}oxy)-3,4,5-trihydroxyoxane-2-carboxylic acid

> <ALOGPS_LOGP>
0.60

> <JCHEM_LOGP>
0.06683792099999972

> <ALOGPS_LOGS>
-2.33

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.476797871381167

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.187119629455068

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6868267697279613

> <JCHEM_POLAR_SURFACE_AREA>
183.20999999999995

> <JCHEM_REFRACTIVITY>
94.89359999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.97e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S,4S,5R,6S)-6-({8,9-dihydroxy-6-oxobenzo[c]chromen-3-yl}oxy)-3,4,5-trihydroxyoxane-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 16-OCT-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-OCT-19         0                                  
HETATM    1  C   UNK     0      -2.104  -0.564   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.564  -0.564   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.104   2.104   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.516  -0.564   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.056   2.104   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.874   0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.206   0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.746   0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.516   2.104   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.056  -0.564   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.826   0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.564   2.104   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -7.494  -1.897   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -6.724  -3.231   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -6.724  -0.564   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -5.184  -3.231   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -4.414  -4.565   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.746   3.437   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -5.184  -0.564   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       4.826  -1.897   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       6.366   0.770   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -9.034  -1.897   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -7.494  -4.565   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -7.494   0.770   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      -2.874  -4.565   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -5.184  -5.898   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       2.516   4.771   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      -4.414   0.770   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       0.206   3.437   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -4.414  -1.897   0.000  0.00  0.00           O+0
HETATM   31  H   UNK     0      -8.264  -3.231   0.000  0.00  0.00           H+0
HETATM   32  H   UNK     0      -5.954  -4.565   0.000  0.00  0.00           H+0
HETATM   33  H   UNK     0      -5.954   0.770   0.000  0.00  0.00           H+0
HETATM   34  H   UNK     0      -5.954  -1.897   0.000  0.00  0.00           H+0
HETATM   35  H   UNK     0      -3.644  -0.564   0.000  0.00  0.00           H+0
CONECT    1    2    6                                                       
CONECT    2    1    7                                                       
CONECT    3    6   12                                                       
CONECT    4    8   10                                                       
CONECT    5    9   11                                                       
CONECT    6    1    3   28                                                  
CONECT    7    2    8   12                                                  
CONECT    8    4    7    9                                                  
CONECT    9    5    8   18                                                  
CONECT   10    4   11   20                                                  
CONECT   11    5   10   21                                                  
CONECT   12    3    7   29                                                  
CONECT   13   14   15   22   31                                             
CONECT   14   13   16   23   32                                             
CONECT   15   13   19   24   33                                             
CONECT   16   14   17   30   34                                             
CONECT   17   16   25   26                                                  
CONECT   18    9   27   29                                                  
CONECT   19   15   28   30   35                                             
CONECT   20   10                                                            
CONECT   21   11                                                            
CONECT   22   13                                                            
CONECT   23   14                                                            
CONECT   24   15                                                            
CONECT   25   17                                                            
CONECT   26   17                                                            
CONECT   27   18                                                            
CONECT   28    6   19                                                       
CONECT   29   12   18                                                       
CONECT   30   16   19                                                       
CONECT   31   13                                                            
CONECT   32   14                                                            
CONECT   33   15                                                            
CONECT   34   16                                                            
CONECT   35   19                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   76    0
END

View in JSmol

Synonyms

Value	Source
(2S,3S,4S,5R,6S)-6-({8,9-dihydroxy-6-oxo-6H-benzo[c]chromen-3-yl}oxy)-3,4,5-trihydroxyoxane-2-carboxylate	Generator
3,8,9-Trihydroxyurolithin 3-glucuronide	HMDB
Urolithin C 3-O-beta-D-glucuronopyranoside	HMDB
Urolithin C 3-O-glucuronide	HMDB
Urolithin C 3-O-β-D-glucuronopyranoside	HMDB
Urolithin C 3-glucuronide	HMDB
6-({8,9-dihydroxy-6-oxo-6H-benzo[c]chromen-3-yl}oxy)-3,4,5-trihydroxyoxane-2-carboxylic acid
8,9-dihydroxy-urolithin-3-glucuronide
urolithin C-3-glucuronide

Chemical Formula

C₁₉H₁₆O₁₁

Average Mass

420.3260 Da

Monoisotopic Mass

420.06926 Da

IUPAC Name

(2S,3S,4S,5R,6S)-6-({8,9-dihydroxy-6-oxo-6H-benzo[c]chromen-3-yl}oxy)-3,4,5-trihydroxyoxane-2-carboxylic acid

Traditional Name

(2S,3S,4S,5R,6S)-6-({8,9-dihydroxy-6-oxobenzo[c]chromen-3-yl}oxy)-3,4,5-trihydroxyoxane-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

[H][C@@]1(OC2=CC3=C(C=C2)C2=CC(O)=C(O)C=C2C(=O)O3)O[C@]([H])(C(O)=O)[C@@]([H])(O)[C@]([H])(O)[C@@]1([H])O

InChI Identifier

InChI=1S/C19H16O11/c20-10-4-8-7-2-1-6(3-12(7)29-18(27)9(8)5-11(10)21)28-19-15(24)13(22)14(23)16(30-19)17(25)26/h1-5,13-16,19-24H,(H,25,26)/t13-,14-,15+,16-,19+/m0/s1

InChI Key

DDAQYQCCOWZGDO-KSPMYQCISA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Phenolic glycosides

Alternative Parents

Substituents

Phenolic glycoside
1-o-glucuronide
O-glucuronide
Glucuronic acid or derivatives
Hexose monosaccharide
Coumarin
Isocoumarin
O-glycosyl compound
2-benzopyran
1-benzopyran
Benzopyran
Pyranone
Beta-hydroxy acid
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Pyran
Oxane
Monosaccharide
Hydroxy acid
Heteroaromatic compound
Secondary alcohol
Lactone
Monocarboxylic acid or derivatives
Acetal
Carboxylic acid
Carboxylic acid derivative
Polyol
Oxacycle
Organoheterocyclic compound
Organic oxide
Hydrocarbon derivative
Carbonyl group
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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	0.6	ALOGPS
logP	0.067	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	3.19	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	183.21 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	94.89 m³·mol⁻¹	ChemAxon
Polarizability	38.92 Å³	ChemAxon
Number of Rings	4	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

HMDB0142405

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Urolithin c 3-glucuronide (NP0334549)

MOL for NP0334549 (Urolithin c 3-glucuronide)

3D MOL for NP0334549 (Urolithin c 3-glucuronide)

3D SDF for NP0334549 (Urolithin c 3-glucuronide)

3D-SDF for NP0334549 (Urolithin c 3-glucuronide)

PDB for NP0334549 (Urolithin c 3-glucuronide)

3D PDB for NP0334549 (Urolithin c 3-glucuronide)

SMILES for NP0334549 (Urolithin c 3-glucuronide)

INCHI for NP0334549 (Urolithin c 3-glucuronide)

Structure for NP0334549 (Urolithin c 3-glucuronide)

3D Structure for NP0334549 (Urolithin c 3-glucuronide)