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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 08:00:19 UTC

Update Date

2021-09-26 23:02:34 UTC

HMDB ID

HMDB0250858

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Daphnoretin

Description

Daphnoretin belongs to the class of organic compounds known as 7-hydroxycoumarins. These are coumarins that contain one or more hydroxyl groups attached to the C7 position the coumarin skeleton. Daphnoretin is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on Daphnoretin. This compound has been identified in human blood as reported by (PMID: 31557052 ). Daphnoretin is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Daphnoretin is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

  Mrv1652309112110002D          

 26 29  0  0  0  0            999 V2000
   -4.2868    2.4750    0.0000 C   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
   -3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    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
   -2.8579   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 O   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
    0.0000   -1.6500    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
    0.0000   -0.0000    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
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013    1.2375    0.0000 O   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
  7  8  2  0  0  0  0
  3  8  1  0  0  0  0
  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
  6 13  1  0  0  0  0
 10 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 15 20  1  0  0  0  0
 18 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 17 25  1  0  0  0  0
  4 26  1  0  0  0  0
M  END

HMDB0250858
     RDKit          3D
Daphnoretin
 38 41  0  0  0  0  0  0  0  0999 V2000
    6.2715    0.7318    1.2460 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8226    1.2935    0.0546 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6118    1.1047   -0.5421 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6632    0.2845    0.0227 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4210    0.0942   -0.5950 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5156   -0.7399    0.0228 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2748   -0.9239   -0.6033 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6859   -1.7439   -0.0478 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9554   -1.3621    0.3456 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1283   -0.7946    1.6153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3477   -0.3861    2.0945 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4657   -0.5335    1.3032 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7234   -0.1335    1.7467 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7810   -0.3185    0.8908 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5861   -0.8780   -0.3506 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6229   -1.0147   -1.0845 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3954   -1.2464   -0.7465 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3394   -1.0864    0.0501 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0840   -1.4927   -0.4093 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0746   -0.2531   -1.7801 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0398   -0.3920   -2.3831 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9950    0.5420   -2.3269 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1593    0.7463   -1.7880 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1096    1.5793   -2.3712 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3363    1.7443   -1.7262 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3005    2.5616   -2.2750 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8611   -0.3039    1.3768 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3864    0.5931    1.1452 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0477    1.3164    2.1477 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8447   -0.2268    0.9408 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7228   -1.2514    0.9601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2495   -0.6814    2.2310 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4888    0.0505    3.0681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8185    0.3026    2.7370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7588   -0.0022    1.2482 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0258   -1.9297   -1.3948 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8966    2.0776   -3.2924 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1810    2.6722   -1.8000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  1  0
 18 19  2  0
  7 20  1  0
 20 21  2  0
 20 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  2  0
 25 26  1  0
 25  3  1  0
 23  5  2  0
 19  9  1  0
 18 12  1  0
  1 27  1  0
  1 28  1  0
  1 29  1  0
  4 30  1  0
  6 31  1  0
 10 32  1  0
 11 33  1  0
 13 34  1  0
 14 35  1  0
 19 36  1  0
 24 37  1  0
 26 38  1  0
M  END

  Mrv1652309112110002D          

 26 29  0  0  0  0            999 V2000
   -4.2868    2.4750    0.0000 C   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
   -3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    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
   -2.8579   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 O   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
    0.0000   -1.6500    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
    0.0000   -0.0000    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
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013    1.2375    0.0000 O   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
  7  8  2  0  0  0  0
  3  8  1  0  0  0  0
  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
  6 13  1  0  0  0  0
 10 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 15 20  1  0  0  0  0
 18 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 17 25  1  0  0  0  0
  4 26  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0250858

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=C(O)C=C2OC(=O)C(OC3=CC4=C(C=CC(=O)O4)C=C3)=CC2=C1

> <INCHI_IDENTIFIER>
InChI=1S/C19H12O7/c1-23-16-6-11-7-17(19(22)26-15(11)9-13(16)20)24-12-4-2-10-3-5-18(21)25-14(10)8-12/h2-9,20H,1H3

> <INCHI_KEY>
JRHMMVBOTXEHGJ-UHFFFAOYSA-N

> <FORMULA>
C19H12O7

> <MOLECULAR_WEIGHT>
352.298

> <EXACT_MASS>
352.058302726

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
33.88542354150285

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
7-hydroxy-6-methoxy-3-[(2-oxo-2H-chromen-7-yl)oxy]-2H-chromen-2-one

> <ALOGPS_LOGP>
3.21

> <JCHEM_LOGP>
2.6892649840000002

> <ALOGPS_LOGS>
-4.48

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.043323531460572

> <JCHEM_PKA_STRONGEST_BASIC>
-4.782896531917336

> <JCHEM_POLAR_SURFACE_AREA>
91.29

> <JCHEM_REFRACTIVITY>
91.71060000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.16e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
daphnoretin

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0250858
     RDKit          3D
Daphnoretin
 38 41  0  0  0  0  0  0  0  0999 V2000
    6.2715    0.7318    1.2460 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8226    1.2935    0.0546 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6118    1.1047   -0.5421 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6632    0.2845    0.0227 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4210    0.0942   -0.5950 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5156   -0.7399    0.0228 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2748   -0.9239   -0.6033 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6859   -1.7439   -0.0478 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9554   -1.3621    0.3456 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1283   -0.7946    1.6153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3477   -0.3861    2.0945 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4657   -0.5335    1.3032 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7234   -0.1335    1.7467 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7810   -0.3185    0.8908 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5861   -0.8780   -0.3506 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6229   -1.0147   -1.0845 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3954   -1.2464   -0.7465 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3394   -1.0864    0.0501 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0840   -1.4927   -0.4093 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0746   -0.2531   -1.7801 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0398   -0.3920   -2.3831 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9950    0.5420   -2.3269 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1593    0.7463   -1.7880 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1096    1.5793   -2.3712 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3363    1.7443   -1.7262 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3005    2.5616   -2.2750 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8611   -0.3039    1.3768 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3864    0.5931    1.1452 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0477    1.3164    2.1477 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8447   -0.2268    0.9408 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7228   -1.2514    0.9601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2495   -0.6814    2.2310 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4888    0.0505    3.0681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8185    0.3026    2.7370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7588   -0.0022    1.2482 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0258   -1.9297   -1.3948 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8966    2.0776   -3.2924 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1810    2.6722   -1.8000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  1  0
 18 19  2  0
  7 20  1  0
 20 21  2  0
 20 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  2  0
 25 26  1  0
 25  3  1  0
 23  5  2  0
 19  9  1  0
 18 12  1  0
  1 27  1  0
  1 28  1  0
  1 29  1  0
  4 30  1  0
  6 31  1  0
 10 32  1  0
 11 33  1  0
 13 34  1  0
 14 35  1  0
 19 36  1  0
 24 37  1  0
 26 38  1  0
M  END

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0      -8.002   4.620   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -6.668   3.850   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -8.002   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -8.002   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -9.336   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5   26                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   13                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7    3                                                       
CONECT    9    7   10                                                       
CONECT   10    9   11   14                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11    6                                                       
CONECT   14   10   15                                                       
CONECT   15   14   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   25                                                  
CONECT   18   17   19   21                                                  
CONECT   19   18   20                                                       
CONECT   20   19   15                                                       
CONECT   21   18   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   17                                                       
CONECT   26    4                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   58    0
END

COMPND    HMDB0250858
HETATM    1  C1  UNL     1       6.271   0.732   1.246  1.00  0.00           C  
HETATM    2  O1  UNL     1       5.823   1.294   0.055  1.00  0.00           O  
HETATM    3  C2  UNL     1       4.612   1.105  -0.542  1.00  0.00           C  
HETATM    4  C3  UNL     1       3.663   0.284   0.023  1.00  0.00           C  
HETATM    5  C4  UNL     1       2.421   0.094  -0.595  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.516  -0.740   0.023  1.00  0.00           C  
HETATM    7  C6  UNL     1       0.275  -0.924  -0.603  1.00  0.00           C  
HETATM    8  O2  UNL     1      -0.686  -1.744  -0.048  1.00  0.00           O  
HETATM    9  C7  UNL     1      -1.955  -1.362   0.346  1.00  0.00           C  
HETATM   10  C8  UNL     1      -2.128  -0.795   1.615  1.00  0.00           C  
HETATM   11  C9  UNL     1      -3.348  -0.386   2.094  1.00  0.00           C  
HETATM   12  C10 UNL     1      -4.466  -0.533   1.303  1.00  0.00           C  
HETATM   13  C11 UNL     1      -5.723  -0.134   1.747  1.00  0.00           C  
HETATM   14  C12 UNL     1      -6.781  -0.318   0.891  1.00  0.00           C  
HETATM   15  C13 UNL     1      -6.586  -0.878  -0.351  1.00  0.00           C  
HETATM   16  O3  UNL     1      -7.623  -1.015  -1.084  1.00  0.00           O  
HETATM   17  O4  UNL     1      -5.395  -1.246  -0.746  1.00  0.00           O  
HETATM   18  C14 UNL     1      -4.339  -1.086   0.050  1.00  0.00           C  
HETATM   19  C15 UNL     1      -3.084  -1.493  -0.409  1.00  0.00           C  
HETATM   20  C16 UNL     1       0.075  -0.253  -1.780  1.00  0.00           C  
HETATM   21  O5  UNL     1      -1.040  -0.392  -2.383  1.00  0.00           O  
HETATM   22  O6  UNL     1       0.995   0.542  -2.327  1.00  0.00           O  
HETATM   23  C17 UNL     1       2.159   0.746  -1.788  1.00  0.00           C  
HETATM   24  C18 UNL     1       3.110   1.579  -2.371  1.00  0.00           C  
HETATM   25  C19 UNL     1       4.336   1.744  -1.726  1.00  0.00           C  
HETATM   26  O7  UNL     1       5.301   2.562  -2.275  1.00  0.00           O  
HETATM   27  H1  UNL     1       5.861  -0.304   1.377  1.00  0.00           H  
HETATM   28  H2  UNL     1       7.386   0.593   1.145  1.00  0.00           H  
HETATM   29  H3  UNL     1       6.048   1.316   2.148  1.00  0.00           H  
HETATM   30  H4  UNL     1       3.845  -0.227   0.941  1.00  0.00           H  
HETATM   31  H5  UNL     1       1.723  -1.251   0.960  1.00  0.00           H  
HETATM   32  H6  UNL     1      -1.249  -0.681   2.231  1.00  0.00           H  
HETATM   33  H7  UNL     1      -3.489   0.051   3.068  1.00  0.00           H  
HETATM   34  H8  UNL     1      -5.818   0.303   2.737  1.00  0.00           H  
HETATM   35  H9  UNL     1      -7.759  -0.002   1.248  1.00  0.00           H  
HETATM   36  H10 UNL     1      -3.026  -1.930  -1.395  1.00  0.00           H  
HETATM   37  H11 UNL     1       2.897   2.078  -3.292  1.00  0.00           H  
HETATM   38  H12 UNL     1       6.181   2.672  -1.800  1.00  0.00           H  
CONECT    1    2   27   28   29
CONECT    2    3
CONECT    3    4    4   25
CONECT    4    5   30
CONECT    5    6   23   23
CONECT    6    7    7   31
CONECT    7    8   20
CONECT    8    9
CONECT    9   10   10   19
CONECT   10   11   32
CONECT   11   12   12   33
CONECT   12   13   18
CONECT   13   14   14   34
CONECT   14   15   35
CONECT   15   16   16   17
CONECT   17   18
CONECT   18   19   19
CONECT   19   36
CONECT   20   21   21   22
CONECT   22   23
CONECT   23   24
CONECT   24   25   25   37
CONECT   25   26
CONECT   26   38
END

HMDB0250858
     RDKit          3D
Daphnoretin
 38 41  0  0  0  0  0  0  0  0999 V2000
    6.2715    0.7318    1.2460 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8226    1.2935    0.0546 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6118    1.1047   -0.5421 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6632    0.2845    0.0227 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4210    0.0942   -0.5950 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5156   -0.7399    0.0228 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2748   -0.9239   -0.6033 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6859   -1.7439   -0.0478 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9554   -1.3621    0.3456 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1283   -0.7946    1.6153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3477   -0.3861    2.0945 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4657   -0.5335    1.3032 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7234   -0.1335    1.7467 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7810   -0.3185    0.8908 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5861   -0.8780   -0.3506 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6229   -1.0147   -1.0845 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3954   -1.2464   -0.7465 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3394   -1.0864    0.0501 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0840   -1.4927   -0.4093 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0746   -0.2531   -1.7801 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0398   -0.3920   -2.3831 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9950    0.5420   -2.3269 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1593    0.7463   -1.7880 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1096    1.5793   -2.3712 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3363    1.7443   -1.7262 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3005    2.5616   -2.2750 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8611   -0.3039    1.3768 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3864    0.5931    1.1452 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0477    1.3164    2.1477 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8447   -0.2268    0.9408 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7228   -1.2514    0.9601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2495   -0.6814    2.2310 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4888    0.0505    3.0681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8185    0.3026    2.7370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7588   -0.0022    1.2482 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0258   -1.9297   -1.3948 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8966    2.0776   -3.2924 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1810    2.6722   -1.8000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 17 18  1  0
 18 19  2  0
  7 20  1  0
 20 21  2  0
 20 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  2  0
 25 26  1  0
 25  3  1  0
 23  5  2  0
 19  9  1  0
 18 12  1  0
  1 27  1  0
  1 28  1  0
  1 29  1  0
  4 30  1  0
  6 31  1  0
 10 32  1  0
 11 33  1  0
 13 34  1  0
 14 35  1  0
 19 36  1  0
 24 37  1  0
 26 38  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
7-Hydroxy-6-methoxy-3,7'-dicoumaryl ether	HMDB

Chemical Formula

C₁₉H₁₂O₇

Average Molecular Weight

352.298

Monoisotopic Molecular Weight

352.058302726

IUPAC Name

7-hydroxy-6-methoxy-3-[(2-oxo-2H-chromen-7-yl)oxy]-2H-chromen-2-one

Traditional Name

daphnoretin

CAS Registry Number

Not Available

SMILES

COC1=C(O)C=C2OC(=O)C(OC3=CC4=C(C=CC(=O)O4)C=C3)=CC2=C1

InChI Identifier

InChI=1S/C19H12O7/c1-23-16-6-11-7-17(19(22)26-15(11)9-13(16)20)24-12-4-2-10-3-5-18(21)25-14(10)8-12/h2-9,20H,1H3

InChI Key

JRHMMVBOTXEHGJ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 7-hydroxycoumarins. These are coumarins that contain one or more hydroxyl groups attached to the C7 position the coumarin skeleton.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Coumarins and derivatives

Sub Class

Hydroxycoumarins

Direct Parent

7-hydroxycoumarins

Alternative Parents

Substituents

7-hydroxycoumarin
Diaryl ether
Benzopyran
1-benzopyran
Anisole
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Pyranone
Pyran
Benzenoid
Heteroaromatic compound
Lactone
Organoheterocyclic compound
Ether
Oxacycle
Organooxygen compound
Hydrocarbon derivative
Organic oxygen compound
Organic oxide
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

aromatic ether (CHEBI:4324 )
hydroxycoumarin (CHEBI:4324 )
coumarins (C09216 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Not Available

Role

Not Available

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	3.21	ALOGPS
logP	2.69	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Acidic)	8.04	ChemAxon
pKa (Strongest Basic)	-4.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	91.29 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	91.71 m³·mol⁻¹	ChemAxon
Polarizability	33.89 Å³	ChemAxon
Number of Rings	4	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
DeepCCS	[M+H]+	185.539	30932474
DeepCCS	[M-H]-	183.181	30932474
DeepCCS	[M-2H]-	217.388	30932474
DeepCCS	[M+Na]+	192.617	30932474
AllCCS	[M+H]+	179.4	32859911
AllCCS	[M+H-H2O]+	176.3	32859911
AllCCS	[M+NH4]+	182.4	32859911
AllCCS	[M+Na]+	183.2	32859911
AllCCS	[M-H]-	180.6	32859911
AllCCS	[M+Na-2H]-	179.5	32859911
AllCCS	[M+HCOO]-	178.4	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Daphnoretin	COC1=C(O)C=C2OC(=O)C(OC3=CC4=C(C=CC(=O)O4)C=C3)=CC2=C1	4460.3	Standard polar	33892256
Daphnoretin	COC1=C(O)C=C2OC(=O)C(OC3=CC4=C(C=CC(=O)O4)C=C3)=CC2=C1	3300.4	Standard non polar	33892256
Daphnoretin	COC1=C(O)C=C2OC(=O)C(OC3=CC4=C(C=CC(=O)O4)C=C3)=CC2=C1	3614.8	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Daphnoretin GC-MS (Non-derivatized) - 70eV, Positive	splash10-05fr-0529000000-3753911b4f1e2df50769	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Daphnoretin GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Daphnoretin GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Daphnoretin GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Daphnoretin 10V, Negative-QTOF	splash10-0udi-0009000000-89013e8d159ca4e9d880	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Daphnoretin 20V, Negative-QTOF	splash10-000i-0309000000-b0178c49c6565fbcc72c	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Daphnoretin 40V, Negative-QTOF	splash10-03di-0900000000-11ff44f0cc734593064c	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Daphnoretin 20V, Positive-QTOF	splash10-0udi-0409000000-03faf24508e7a8da13fe	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Daphnoretin 10V, Positive-QTOF	splash10-0udi-0009000000-60268f1d430b1e4a9906	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Daphnoretin 10V, Negative-QTOF	splash10-0udi-0009000000-fbaae7d8d0a33f870dc0	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Daphnoretin 20V, Negative-QTOF	splash10-0udi-0009000000-c81b6d7b0f0b4898c6e4	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Daphnoretin 40V, Negative-QTOF	splash10-0bt9-0956000000-108a3565396e2eec71a4	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Daphnoretin 10V, Positive-QTOF	splash10-0udi-0009000000-6b09288367f287c3aa7b	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Daphnoretin 20V, Positive-QTOF	splash10-0udi-0009000000-8af4622b35ba97adea5d	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Daphnoretin 40V, Positive-QTOF	splash10-0a4i-0679000000-75e077f05ee87603bb53	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

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

Not Available

KNApSAcK ID

C00002463

Chemspider ID

4444756

KEGG Compound ID

C09216

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Daphnoretin

METLIN ID

Not Available

PubChem Compound

5281406

PDB ID

Not Available

ChEBI ID

4324

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

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for Daphnoretin (HMDB0250858)

MOL for HMDB0250858 (Daphnoretin)

3D MOL for HMDB0250858 (Daphnoretin)

3D SDF for HMDB0250858 (Daphnoretin)

3D-SDF for HMDB0250858 (Daphnoretin)

PDB for HMDB0250858 (Daphnoretin)

3D PDB for HMDB0250858 (Daphnoretin)

SMILES for HMDB0250858 (Daphnoretin)

INCHI for HMDB0250858 (Daphnoretin)

Structure for HMDB0250858 (Daphnoretin)

3D Structure for HMDB0250858 (Daphnoretin)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra