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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-09-23 18:40:58 UTC

Update Date

2021-09-23 18:40:58 UTC

HMDB ID

HMDB0302555

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Nordentatin

Description

Nordentatin is a member of the class of compounds known as angular pyranocoumarins. Angular pyranocoumarins are organic compounds containing a pyran (or a hydrogenated derivative) angularly fused to a coumarin moiety. Nordentatin is practically insoluble (in water) and a very weakly acidic compound (based on its pKa). Nordentatin can be found in sweet orange, which makes nordentatin a potential biomarker for the consumption of this food product.

Structure

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

HMDB0302555
     RDKit          3D
Nordentatin
 43 45  0  0  0  0  0  0  0  0999 V2000
   -4.3595    0.2438    1.8681 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3053    0.5956    1.1661 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8596   -0.1711   -0.0354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6269    0.3685   -1.1963 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1838   -1.6468    0.2157 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3922   -0.0353   -0.1495 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6108   -0.4969    0.9140 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2644   -1.0511    2.0050 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7813   -0.4012    0.8749 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3738    0.1638   -0.2460 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6279    0.6241   -1.3025 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2421    1.1890   -2.4205 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4522    1.6301   -3.4419 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9173    1.4969   -3.3211 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6324    1.9154   -4.2860 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4208    0.9637   -2.2570 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7531    0.5111   -1.2257 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7347    0.2640   -0.2981 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6112   -0.1686    0.7155 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3976    1.0366    1.1826 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5134   -1.2235    0.1110 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9232   -0.7519    1.8637 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5893   -0.8788    1.9752 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9541   -0.6268    1.5996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6595    0.8131    2.7295 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7259    1.4631    1.4459 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4519   -0.1452   -2.1562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7047    0.1973   -0.9695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4629    1.4453   -1.2728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3065   -2.2619   -0.0856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0436   -1.9720   -0.4159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3447   -1.8404    1.2921 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7786   -1.3975    2.7912 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3152    1.2657   -2.4568 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8563    2.0806   -4.3436 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1344    0.7731    1.9705 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8703    1.4800    0.2888 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6646    1.7723    1.5613 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8216   -1.9832   -0.3577 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1162   -1.7570    0.8511 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0817   -0.7934   -0.7280 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4986   -1.1125    2.6905 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1529   -1.3201    2.8536 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  3  5  1  0
  3  6  1  0
  6  7  2  0
  7  8  1  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 10 18  1  0
 18 19  1  0
 19 20  1  0
 19 21  1  0
 19 22  1  0
 22 23  2  0
 17  6  1  0
 23  9  1  0
 17 11  2  0
  1 24  1  0
  1 25  1  0
  2 26  1  0
  4 27  1  0
  4 28  1  0
  4 29  1  0
  5 30  1  0
  5 31  1  0
  5 32  1  0
  8 33  1  0
 12 34  1  0
 13 35  1  0
 20 36  1  0
 20 37  1  0
 20 38  1  0
 21 39  1  0
 21 40  1  0
 21 41  1  0
 22 42  1  0
 23 43  1  0
M  END


  Mrv0541 02241221082D          

 23 25  0  0  0  0            999 V2000
    3.4587    1.9394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6020    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6020   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770    1.1270    0.0000 O   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
    1.1270   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7770   -1.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -1.3184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.4454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8414   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8414   -2.9684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -0.3020    0.0000 O   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 O   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
    1.1270    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3772    1.4091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  5 11  1  0  0  0  0
 11 12  1  0  0  0  0
 10 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 13 16  1  0  0  0  0
 16 17  2  0  0  0  0
  9 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
 21 22  2  0  0  0  0
  8 22  1  0  0  0  0
  2 23  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0302555

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)(C=C)C1=C(O)C2=C(OC(C)(C)C=C2)C2=C1OC(=O)C=C2

> <INCHI_IDENTIFIER>
InChI=1S/C19H20O4/c1-6-18(2,3)14-15(21)11-9-10-19(4,5)23-16(11)12-7-8-13(20)22-17(12)14/h6-10,21H,1H2,2-5H3

> <INCHI_KEY>
FREXEHTVBRSRGJ-UHFFFAOYSA-N

> <FORMULA>
C19H20O4

> <MOLECULAR_WEIGHT>
312.3597

> <EXACT_MASS>
312.136159128

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
33.659500770693

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-hydroxy-2,2-dimethyl-6-(2-methylbut-3-en-2-yl)-2H,8H-pyrano[2,3-h]chromen-8-one

> <ALOGPS_LOGP>
4.47

> <JCHEM_LOGP>
4.0660546449999995

> <ALOGPS_LOGS>
-4.42

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.5688895105696545

> <JCHEM_PKA_STRONGEST_BASIC>
-4.937648530456829

> <JCHEM_POLAR_SURFACE_AREA>
55.76

> <JCHEM_REFRACTIVITY>
91.2339

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.18e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-hydroxy-2,2-dimethyl-6-(2-methylbut-3-en-2-yl)pyrano[2,3-h]chromen-8-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0302555
     RDKit          3D
Nordentatin
 43 45  0  0  0  0  0  0  0  0999 V2000
   -4.3595    0.2438    1.8681 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3053    0.5956    1.1661 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8596   -0.1711   -0.0354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6269    0.3685   -1.1963 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1838   -1.6468    0.2157 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3922   -0.0353   -0.1495 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6108   -0.4969    0.9140 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2644   -1.0511    2.0050 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7813   -0.4012    0.8749 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3738    0.1638   -0.2460 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6279    0.6241   -1.3025 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2421    1.1890   -2.4205 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4522    1.6301   -3.4419 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9173    1.4969   -3.3211 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6324    1.9154   -4.2860 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4208    0.9637   -2.2570 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7531    0.5111   -1.2257 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7347    0.2640   -0.2981 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6112   -0.1686    0.7155 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3976    1.0366    1.1826 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5134   -1.2235    0.1110 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9232   -0.7519    1.8637 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5893   -0.8788    1.9752 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9541   -0.6268    1.5996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6595    0.8131    2.7295 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7259    1.4631    1.4459 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4519   -0.1452   -2.1562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7047    0.1973   -0.9695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4629    1.4453   -1.2728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3065   -2.2619   -0.0856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0436   -1.9720   -0.4159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3447   -1.8404    1.2921 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7786   -1.3975    2.7912 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3152    1.2657   -2.4568 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8563    2.0806   -4.3436 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1344    0.7731    1.9705 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8703    1.4800    0.2888 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6646    1.7723    1.5613 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8216   -1.9832   -0.3577 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1162   -1.7570    0.8511 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0817   -0.7934   -0.7280 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4986   -1.1125    2.6905 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1529   -1.3201    2.8536 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  3  5  1  0
  3  6  1  0
  6  7  2  0
  7  8  1  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 10 18  1  0
 18 19  1  0
 19 20  1  0
 19 21  1  0
 19 22  1  0
 22 23  2  0
 17  6  1  0
 23  9  1  0
 17 11  2  0
  1 24  1  0
  1 25  1  0
  2 26  1  0
  4 27  1  0
  4 28  1  0
  4 29  1  0
  5 30  1  0
  5 31  1  0
  5 32  1  0
  8 33  1  0
 12 34  1  0
 13 35  1  0
 20 36  1  0
 20 37  1  0
 20 38  1  0
 21 39  1  0
 21 40  1  0
 21 41  1  0
 22 42  1  0
 23 43  1  0
M  END

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       6.456   3.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.724   2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.494   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.724  -0.564   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.184  -0.564   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.414   0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       5.184   2.104   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.104  -0.564   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.874  -1.897   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.414  -1.897   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       5.184  -3.231   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       2.104  -3.231   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.770  -2.461   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.334  -4.565   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.437  -4.001   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.437  -5.541   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       0.564  -0.564   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -0.206   0.770   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -1.746   0.770   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       0.564   2.104   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.104   2.104   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.171   2.630   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    7   23                                             
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   11                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6    2                                                       
CONECT    8    6    9   22                                                  
CONECT    9    8   10   18                                                  
CONECT   10    9   11   13                                                  
CONECT   11   10    5   12                                                  
CONECT   12   11                                                            
CONECT   13   10   14   15   16                                             
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   13   17                                                       
CONECT   17   16                                                            
CONECT   18    9   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21    8                                                       
CONECT   23    2                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   50    0
END

COMPND    HMDB0302555
HETATM    1  C1  UNL     1      -4.359   0.244   1.868  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.305   0.596   1.166  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.860  -0.171  -0.035  1.00  0.00           C  
HETATM    4  C4  UNL     1      -3.627   0.368  -1.196  1.00  0.00           C  
HETATM    5  C5  UNL     1      -3.184  -1.647   0.216  1.00  0.00           C  
HETATM    6  C6  UNL     1      -1.392  -0.035  -0.149  1.00  0.00           C  
HETATM    7  C7  UNL     1      -0.611  -0.497   0.914  1.00  0.00           C  
HETATM    8  O1  UNL     1      -1.264  -1.051   2.005  1.00  0.00           O  
HETATM    9  C8  UNL     1       0.781  -0.401   0.875  1.00  0.00           C  
HETATM   10  C9  UNL     1       1.374   0.164  -0.246  1.00  0.00           C  
HETATM   11  C10 UNL     1       0.628   0.624  -1.302  1.00  0.00           C  
HETATM   12  C11 UNL     1       1.242   1.189  -2.421  1.00  0.00           C  
HETATM   13  C12 UNL     1       0.452   1.630  -3.442  1.00  0.00           C  
HETATM   14  C13 UNL     1      -0.917   1.497  -3.321  1.00  0.00           C  
HETATM   15  O2  UNL     1      -1.632   1.915  -4.286  1.00  0.00           O  
HETATM   16  O3  UNL     1      -1.421   0.964  -2.257  1.00  0.00           O  
HETATM   17  C14 UNL     1      -0.753   0.511  -1.226  1.00  0.00           C  
HETATM   18  O4  UNL     1       2.735   0.264  -0.298  1.00  0.00           O  
HETATM   19  C15 UNL     1       3.611  -0.169   0.716  1.00  0.00           C  
HETATM   20  C16 UNL     1       4.398   1.037   1.183  1.00  0.00           C  
HETATM   21  C17 UNL     1       4.513  -1.224   0.111  1.00  0.00           C  
HETATM   22  C18 UNL     1       2.923  -0.752   1.864  1.00  0.00           C  
HETATM   23  C19 UNL     1       1.589  -0.879   1.975  1.00  0.00           C  
HETATM   24  H1  UNL     1      -4.954  -0.627   1.600  1.00  0.00           H  
HETATM   25  H2  UNL     1      -4.660   0.813   2.729  1.00  0.00           H  
HETATM   26  H3  UNL     1      -2.726   1.463   1.446  1.00  0.00           H  
HETATM   27  H4  UNL     1      -3.452  -0.145  -2.156  1.00  0.00           H  
HETATM   28  H5  UNL     1      -4.705   0.197  -0.970  1.00  0.00           H  
HETATM   29  H6  UNL     1      -3.463   1.445  -1.273  1.00  0.00           H  
HETATM   30  H7  UNL     1      -2.306  -2.262  -0.086  1.00  0.00           H  
HETATM   31  H8  UNL     1      -4.044  -1.972  -0.416  1.00  0.00           H  
HETATM   32  H9  UNL     1      -3.345  -1.840   1.292  1.00  0.00           H  
HETATM   33  H10 UNL     1      -0.779  -1.397   2.791  1.00  0.00           H  
HETATM   34  H11 UNL     1       2.315   1.266  -2.457  1.00  0.00           H  
HETATM   35  H12 UNL     1       0.856   2.081  -4.344  1.00  0.00           H  
HETATM   36  H13 UNL     1       5.134   0.773   1.970  1.00  0.00           H  
HETATM   37  H14 UNL     1       4.870   1.480   0.289  1.00  0.00           H  
HETATM   38  H15 UNL     1       3.665   1.772   1.561  1.00  0.00           H  
HETATM   39  H16 UNL     1       3.822  -1.983  -0.358  1.00  0.00           H  
HETATM   40  H17 UNL     1       5.116  -1.757   0.851  1.00  0.00           H  
HETATM   41  H18 UNL     1       5.082  -0.793  -0.728  1.00  0.00           H  
HETATM   42  H19 UNL     1       3.499  -1.113   2.690  1.00  0.00           H  
HETATM   43  H20 UNL     1       1.153  -1.320   2.854  1.00  0.00           H  
CONECT    1    2    2   24   25
CONECT    2    3   26
CONECT    3    4    5    6
CONECT    4   27   28   29
CONECT    5   30   31   32
CONECT    6    7    7   17
CONECT    7    8    9
CONECT    8   33
CONECT    9   10   10   23
CONECT   10   11   18
CONECT   11   12   17   17
CONECT   12   13   13   34
CONECT   13   14   35
CONECT   14   15   15   16
CONECT   16   17
CONECT   18   19
CONECT   19   20   21   22
CONECT   20   36   37   38
CONECT   21   39   40   41
CONECT   22   23   23   42
CONECT   23   43
END

HMDB0302555
     RDKit          3D
Nordentatin
 43 45  0  0  0  0  0  0  0  0999 V2000
   -4.3595    0.2438    1.8681 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3053    0.5956    1.1661 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8596   -0.1711   -0.0354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6269    0.3685   -1.1963 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1838   -1.6468    0.2157 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3922   -0.0353   -0.1495 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6108   -0.4969    0.9140 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2644   -1.0511    2.0050 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7813   -0.4012    0.8749 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3738    0.1638   -0.2460 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6279    0.6241   -1.3025 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2421    1.1890   -2.4205 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4522    1.6301   -3.4419 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9173    1.4969   -3.3211 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6324    1.9154   -4.2860 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4208    0.9637   -2.2570 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7531    0.5111   -1.2257 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7347    0.2640   -0.2981 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6112   -0.1686    0.7155 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3976    1.0366    1.1826 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5134   -1.2235    0.1110 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9232   -0.7519    1.8637 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5893   -0.8788    1.9752 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9541   -0.6268    1.5996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6595    0.8131    2.7295 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7259    1.4631    1.4459 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4519   -0.1452   -2.1562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7047    0.1973   -0.9695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4629    1.4453   -1.2728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3065   -2.2619   -0.0856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0436   -1.9720   -0.4159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3447   -1.8404    1.2921 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7786   -1.3975    2.7912 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3152    1.2657   -2.4568 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8563    2.0806   -4.3436 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1344    0.7731    1.9705 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8703    1.4800    0.2888 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6646    1.7723    1.5613 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8216   -1.9832   -0.3577 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1162   -1.7570    0.8511 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0817   -0.7934   -0.7280 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4986   -1.1125    2.6905 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1529   -1.3201    2.8536 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  3  5  1  0
  3  6  1  0
  6  7  2  0
  7  8  1  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 10 18  1  0
 18 19  1  0
 19 20  1  0
 19 21  1  0
 19 22  1  0
 22 23  2  0
 17  6  1  0
 23  9  1  0
 17 11  2  0
  1 24  1  0
  1 25  1  0
  2 26  1  0
  4 27  1  0
  4 28  1  0
  4 29  1  0
  5 30  1  0
  5 31  1  0
  5 32  1  0
  8 33  1  0
 12 34  1  0
 13 35  1  0
 20 36  1  0
 20 37  1  0
 20 38  1  0
 21 39  1  0
 21 40  1  0
 21 41  1  0
 22 42  1  0
 23 43  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₉H₂₀O₄

Average Molecular Weight

312.3597

Monoisotopic Molecular Weight

312.136159128

IUPAC Name

5-hydroxy-2,2-dimethyl-6-(2-methylbut-3-en-2-yl)-2H,8H-pyrano[2,3-h]chromen-8-one

Traditional Name

5-hydroxy-2,2-dimethyl-6-(2-methylbut-3-en-2-yl)pyrano[2,3-h]chromen-8-one

CAS Registry Number

Not Available

SMILES

CC(C)(C=C)C1=C(O)C2=C(OC(C)(C)C=C2)C2=C1OC(=O)C=C2

InChI Identifier

InChI=1S/C19H20O4/c1-6-18(2,3)14-15(21)11-9-10-19(4,5)23-16(11)12-7-8-13(20)22-17(12)14/h6-10,21H,1H2,2-5H3

InChI Key

FREXEHTVBRSRGJ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as angular pyranocoumarins. These are organic compounds containing a pyran (or a hydrogenated derivative) angularly fused to a coumarin moiety.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Coumarins and derivatives

Sub Class

Pyranocoumarins

Direct Parent

Angular pyranocoumarins

Alternative Parents

Substituents

Angular pyranocoumarin
2,2-dimethyl-1-benzopyran
Benzopyran
1-benzopyran
Alkyl aryl ether
Pyranone
Pyran
Benzenoid
Heteroaromatic compound
Lactone
Oxacycle
Ether
Organoheterocyclic compound
Hydrocarbon derivative
Organooxygen compound
Organic oxygen compound
Organic oxide
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Exogenous (HMDB: HMDB0302555)

Food

Fruit

Citrus

Sweet orange (FooDB: FOOD00057)

Process

Not Available

Role

Biological role

Anti bacterial (HMDB: HMDB0302555)

Physical Properties

State

Not Available

Experimental Molecular 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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	4.47	ALOGPS
logP	4.07	ChemAxon
logS	-4.4	ALOGPS
pKa (Strongest Acidic)	7.57	ChemAxon
pKa (Strongest Basic)	-4.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	55.76 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	91.23 m³·mol⁻¹	ChemAxon
Polarizability	33.66 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
AllCCS	[M+H]+	171.135	32859911
AllCCS	[M+H-H2O]+	167.712	32859911
AllCCS	[M+Na]+	175.223	32859911
AllCCS	[M+NH4]+	174.31	32859911
AllCCS	[M-H]-	179.623	32859911
AllCCS	[M+Na-2H]-	179.069	32859911
AllCCS	[M+HCOO]-	178.601	32859911
DeepCCS	[M+H]+	179.813	30932474
DeepCCS	[M-H]-	177.455	30932474
DeepCCS	[M-2H]-	211.496	30932474
DeepCCS	[M+Na]+	186.842	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	16.589 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	0.87 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2656.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	427.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	210.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	213.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	130.6 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	722.3 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	807.9 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	71.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1426.6 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	501.7 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1425.5 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	494.2 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	389.5 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	369.4 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	476.3 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	8.1 seconds	40023050

Predicted Kovats Retention Indices

Not Available

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nordentatin 10V, Positive-QTOF	splash10-03di-1039000000-04ab0885c0d0ba6c38c9	2016-08-02	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nordentatin 20V, Positive-QTOF	splash10-02ta-5094000000-904e5a1407a35e65bb52	2016-08-02	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nordentatin 40V, Positive-QTOF	splash10-014i-5090000000-aae2e5e8bf3784f9fda0	2016-08-02	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nordentatin 10V, Negative-QTOF	splash10-03di-0039000000-be416faf7b3766a392d6	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nordentatin 20V, Negative-QTOF	splash10-03di-0096000000-9a7a8353e04792b827ad	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nordentatin 40V, Negative-QTOF	splash10-00o1-3790000000-cbe9d8005775c8e00551	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nordentatin 10V, Positive-QTOF	splash10-03di-0009000000-a87b5d3fcea67318e943	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nordentatin 20V, Positive-QTOF	splash10-01p9-0093000000-345e125de1a85eb61984	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nordentatin 40V, Positive-QTOF	splash10-0zfr-0290000000-7abc8c606fa09794c7c3	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nordentatin 10V, Negative-QTOF	splash10-03di-0009000000-1436f13e3f3f2b9feffe	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nordentatin 20V, Negative-QTOF	splash10-08fu-0049000000-cc897d736d34545e9723	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Nordentatin 40V, Negative-QTOF	splash10-0fbc-0090000000-0174d3df368002517e79	2021-10-21	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB005139

KNApSAcK ID

C00030835

Chemspider ID

4478353

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

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for Nordentatin (HMDB0302555)

MOL for HMDB0302555 (Nordentatin)

3D MOL for HMDB0302555 (Nordentatin)

3D SDF for HMDB0302555 (Nordentatin)

3D-SDF for HMDB0302555 (Nordentatin)

PDB for HMDB0302555 (Nordentatin)

3D PDB for HMDB0302555 (Nordentatin)

SMILES for HMDB0302555 (Nordentatin)

INCHI for HMDB0302555 (Nordentatin)

Structure for HMDB0302555 (Nordentatin)

3D Structure for HMDB0302555 (Nordentatin)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

MS/MS Spectra