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Showing metabocard for Lignan (HMDB0254088)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 13:14:04 UTC
Update Date2021-10-01 22:08:22 UTC
HMDB IDHMDB0254088
Secondary Accession NumbersNone
Metabolite Identification
Common NameLignan
DescriptionLignan, also known as neolignan, belongs to the class of organic compounds known as aryltetralin lignans. These are lignans with a structure based on the 1-phenyltetralin skeleton. Based on a literature review a significant number of articles have been published on Lignan. This compound has been identified in human blood as reported by (PMID: 31557052 ). Lignan is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Lignan 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0254088 (Lignan)


  Mrv1652309112115142D          

 33 35  0  0  0  0            999 V2000
   -1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 O   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 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
    0.7145   -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
    1.4289    0.8250    0.0000 O   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
    2.8579    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
    3.5724   -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
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.0000    0.0000 O   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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 31 32  1  0  0  0  0
  7 33  1  0  0  0  0
M  END
Download

3D MOL for HMDB0254088 (Lignan)

HMDB0254088
     RDKit          3D
Lignan
 63 65  0  0  0  0  0  0  0  0999 V2000
   -4.0499   -4.4834   -0.8671 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7452   -4.3475   -0.1135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4738   -3.0039    0.2281 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3116   -2.7355    0.9199 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5585   -3.6973    1.2083 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9132   -1.3660    1.3366 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9624   -0.7944    2.2320 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8235   -1.3633    3.6247 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8296    0.6775    2.3443 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8765    1.3207    3.4283 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6325    1.4145    1.1080 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0302    2.7250    0.9471 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8417    3.4148   -0.2336 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2412    4.7224   -0.3868 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8671    5.5060    0.5863 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2374    2.7977   -1.3072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0361    3.4833   -2.5204 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4088    2.7837   -3.5789 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8376    1.4912   -1.1557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0288    0.7881    0.0457 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5704   -0.5969    0.1261 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9198   -0.5651   -0.1010 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7766   -0.2613    0.9356 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1682   -0.2227    0.7748 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9972    0.0889    1.8501 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5078    0.3780    3.1331 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6973   -0.4979   -0.4627 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0600   -0.4690   -0.6561 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8007    0.6573   -1.0427 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8554   -0.8018   -1.5036 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3307   -1.0867   -2.7682 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5227   -1.4020   -3.8631 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4747   -0.8360   -1.3269 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.3556   -0.6606    4.3072 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5095    3.2017    1.8134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1902    6.1100    1.1957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5924    6.1895    0.0544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5257    4.8888    1.2650 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0341    1.8640   -3.7653 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.5886    2.3613   -3.2605 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3597    1.0079   -2.0098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9849   -1.1066   -0.7993 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4332   -0.0325    1.9343 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6650    1.1270    3.0695 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1314   -0.5628    3.6198 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2804    0.8840    3.7470 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5045    0.4054   -1.8488 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4324    0.9794   -0.1681 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1563    1.5124   -1.3700 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9845   -0.5288   -4.2889 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8069   -2.2044   -3.5226 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1294   -1.8839   -4.6626 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8134   -1.0755   -2.1435 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
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  3  4  1  0
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  4  6  1  0
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 11 12  2  0
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 13 14  1  0
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 30 31  1  0
 31 32  1  0
 30 33  2  0
 21  6  1  0
 33 22  1  0
 20 11  1  0
  1 34  1  0
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  1 36  1  0
  2 37  1  0
  2 38  1  0
  6 39  1  0
  7 40  1  0
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 29 57  1  0
 29 58  1  0
 29 59  1  0
 32 60  1  0
 32 61  1  0
 32 62  1  0
 33 63  1  0
M  END
Download

3D SDF for HMDB0254088 (Lignan)


  Mrv1652309112115142D          

 33 35  0  0  0  0            999 V2000
   -1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 O   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 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
    0.7145   -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
    1.4289    0.8250    0.0000 O   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
    2.8579    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
    3.5724   -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
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    4.2868   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.0000    0.0000 O   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
    0.0000    0.0000    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  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
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 21 22  2  0  0  0  0
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 23 24  1  0  0  0  0
 20 25  1  0  0  0  0
 25 26  1  0  0  0  0
 19 27  1  0  0  0  0
 27 28  1  0  0  0  0
 13 29  1  0  0  0  0
 29 30  1  0  0  0  0
 12 31  1  0  0  0  0
 31 32  1  0  0  0  0
  7 33  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0254088

> <DATABASE_NAME>
hmdb

> <SMILES>
CCOC(=O)C1C(C)C(=O)C2=CC(OC)=C(OC)C=C2C1C1=CC(OC)=C(OC)C(OC)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C25H30O8/c1-8-33-25(27)21-13(2)23(26)16-12-18(29-4)17(28-3)11-15(16)22(21)14-9-19(30-5)24(32-7)20(10-14)31-6/h9-13,21-22H,8H2,1-7H3

> <INCHI_KEY>
PEIBIXYUYBVLDS-UHFFFAOYSA-N

> <FORMULA>
C25H30O8

> <MOLECULAR_WEIGHT>
458.507

> <EXACT_MASS>
458.194067926

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
48.70111360999977

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
ethyl 6,7-dimethoxy-3-methyl-4-oxo-1-(3,4,5-trimethoxyphenyl)-1,2,3,4-tetrahydronaphthalene-2-carboxylate

> <ALOGPS_LOGP>
3.90

> <JCHEM_LOGP>
3.182024211333333

> <ALOGPS_LOGS>
-5.00

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.420694659244145

> <JCHEM_PKA_STRONGEST_BASIC>
-4.21597446366078

> <JCHEM_POLAR_SURFACE_AREA>
89.52000000000002

> <JCHEM_REFRACTIVITY>
121.6184

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.55e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
lignan

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0254088 (Lignan)

HMDB0254088
     RDKit          3D
Lignan
 63 65  0  0  0  0  0  0  0  0999 V2000
   -4.0499   -4.4834   -0.8671 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7452   -4.3475   -0.1135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4738   -3.0039    0.2281 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3116   -2.7355    0.9199 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5585   -3.6973    1.2083 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9132   -1.3660    1.3366 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9624   -0.7944    2.2320 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8235   -1.3633    3.6247 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8296    0.6775    2.3443 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8765    1.3207    3.4283 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6325    1.4145    1.1080 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0302    2.7250    0.9471 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8417    3.4148   -0.2336 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2412    4.7224   -0.3868 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8671    5.5060    0.5863 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2374    2.7977   -1.3072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0361    3.4833   -2.5204 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4088    2.7837   -3.5789 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8376    1.4912   -1.1557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0288    0.7881    0.0457 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5704   -0.5969    0.1261 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9198   -0.5651   -0.1010 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7766   -0.2613    0.9356 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1682   -0.2227    0.7748 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9972    0.0889    1.8501 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5078    0.3780    3.1331 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6973   -0.4979   -0.4627 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0600   -0.4690   -0.6561 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8007    0.6573   -1.0427 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8554   -0.8018   -1.5036 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3307   -1.0867   -2.7682 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5227   -1.4020   -3.8631 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4747   -0.8360   -1.3269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4024   -5.5240   -0.7221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8506   -4.2424   -1.9335 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8273   -3.8173   -0.4275 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8019   -4.9729    0.7744 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9523   -4.7420   -0.7907 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0150   -1.4748    1.9700 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9943   -1.0257    1.8906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3145   -2.3426    3.6528 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7822   -1.4363    3.9584 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3556   -0.6606    4.3072 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5095    3.2017    1.8134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1902    6.1100    1.1957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5924    6.1895    0.0544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5257    4.8888    1.2650 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0341    1.8640   -3.7653 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2988    3.3832   -4.4812 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5886    2.3613   -3.2605 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3597    1.0079   -2.0098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9849   -1.1066   -0.7993 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4332   -0.0325    1.9343 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6650    1.1270    3.0695 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1314   -0.5628    3.6198 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2804    0.8840    3.7470 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5045    0.4054   -1.8488 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4324    0.9794   -0.1681 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1563    1.5124   -1.3700 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9845   -0.5288   -4.2889 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8069   -2.2044   -3.5226 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1294   -1.8839   -4.6626 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8134   -1.0755   -2.1435 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  2  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 13 16  2  0
 16 17  1  0
 17 18  1  0
 16 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  1  0
 22 23  2  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 24 27  2  0
 27 28  1  0
 28 29  1  0
 27 30  1  0
 30 31  1  0
 31 32  1  0
 30 33  2  0
 21  6  1  0
 33 22  1  0
 20 11  1  0
  1 34  1  0
  1 35  1  0
  1 36  1  0
  2 37  1  0
  2 38  1  0
  6 39  1  0
  7 40  1  0
  8 41  1  0
  8 42  1  0
  8 43  1  0
 12 44  1  0
 15 45  1  0
 15 46  1  0
 15 47  1  0
 18 48  1  0
 18 49  1  0
 18 50  1  0
 19 51  1  0
 21 52  1  0
 23 53  1  0
 26 54  1  0
 26 55  1  0
 26 56  1  0
 29 57  1  0
 29 58  1  0
 29 59  1  0
 32 60  1  0
 32 61  1  0
 32 62  1  0
 33 63  1  0
M  END
Download

PDB for HMDB0254088 (Lignan)

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      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       0.000  -7.700   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       2.667  -9.240   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       5.335  -7.700   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       8.002  -0.000   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   16                                                  
CONECT    7    6    8   33                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   31                                                  
CONECT   13   12   14   29                                                  
CONECT   14   13   15                                                       
CONECT   15   14   10   16                                                  
CONECT   16   15    6   17                                                  
CONECT   17   16   18   22                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   27                                                  
CONECT   20   19   21   25                                                  
CONECT   21   20   22   23                                                  
CONECT   22   21   17                                                       
CONECT   23   21   24                                                       
CONECT   24   23                                                            
CONECT   25   20   26                                                       
CONECT   26   25                                                            
CONECT   27   19   28                                                       
CONECT   28   27                                                            
CONECT   29   13   30                                                       
CONECT   30   29                                                            
CONECT   31   12   32                                                       
CONECT   32   31                                                            
CONECT   33    7                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   70    0
END
Download

3D PDB for HMDB0254088 (Lignan)

COMPND    HMDB0254088
HETATM    1  C1  UNL     1      -4.050  -4.483  -0.867  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.745  -4.348  -0.114  1.00  0.00           C  
HETATM    3  O1  UNL     1      -2.474  -3.004   0.228  1.00  0.00           O  
HETATM    4  C3  UNL     1      -1.312  -2.735   0.920  1.00  0.00           C  
HETATM    5  O2  UNL     1      -0.558  -3.697   1.208  1.00  0.00           O  
HETATM    6  C4  UNL     1      -0.913  -1.366   1.337  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.962  -0.794   2.232  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.823  -1.363   3.625  1.00  0.00           C  
HETATM    9  C7  UNL     1      -1.830   0.678   2.344  1.00  0.00           C  
HETATM   10  O3  UNL     1      -1.876   1.321   3.428  1.00  0.00           O  
HETATM   11  C8  UNL     1      -1.633   1.415   1.108  1.00  0.00           C  
HETATM   12  C9  UNL     1      -2.030   2.725   0.947  1.00  0.00           C  
HETATM   13  C10 UNL     1      -1.842   3.415  -0.234  1.00  0.00           C  
HETATM   14  O4  UNL     1      -2.241   4.722  -0.387  1.00  0.00           O  
HETATM   15  C11 UNL     1      -2.867   5.506   0.586  1.00  0.00           C  
HETATM   16  C12 UNL     1      -1.237   2.798  -1.307  1.00  0.00           C  
HETATM   17  O5  UNL     1      -1.036   3.483  -2.520  1.00  0.00           O  
HETATM   18  C13 UNL     1      -0.409   2.784  -3.579  1.00  0.00           C  
HETATM   19  C14 UNL     1      -0.838   1.491  -1.156  1.00  0.00           C  
HETATM   20  C15 UNL     1      -1.029   0.788   0.046  1.00  0.00           C  
HETATM   21  C16 UNL     1      -0.570  -0.597   0.126  1.00  0.00           C  
HETATM   22  C17 UNL     1       0.920  -0.565  -0.101  1.00  0.00           C  
HETATM   23  C18 UNL     1       1.777  -0.261   0.936  1.00  0.00           C  
HETATM   24  C19 UNL     1       3.168  -0.223   0.775  1.00  0.00           C  
HETATM   25  O6  UNL     1       3.997   0.089   1.850  1.00  0.00           O  
HETATM   26  C20 UNL     1       3.508   0.378   3.133  1.00  0.00           C  
HETATM   27  C21 UNL     1       3.697  -0.498  -0.463  1.00  0.00           C  
HETATM   28  O7  UNL     1       5.060  -0.469  -0.656  1.00  0.00           O  
HETATM   29  C22 UNL     1       5.801   0.657  -1.043  1.00  0.00           C  
HETATM   30  C23 UNL     1       2.855  -0.802  -1.504  1.00  0.00           C  
HETATM   31  O8  UNL     1       3.331  -1.087  -2.768  1.00  0.00           O  
HETATM   32  C24 UNL     1       2.523  -1.402  -3.863  1.00  0.00           C  
HETATM   33  C25 UNL     1       1.475  -0.836  -1.327  1.00  0.00           C  
HETATM   34  H1  UNL     1      -4.402  -5.524  -0.722  1.00  0.00           H  
HETATM   35  H2  UNL     1      -3.851  -4.242  -1.933  1.00  0.00           H  
HETATM   36  H3  UNL     1      -4.827  -3.817  -0.428  1.00  0.00           H  
HETATM   37  H4  UNL     1      -2.802  -4.973   0.774  1.00  0.00           H  
HETATM   38  H5  UNL     1      -1.952  -4.742  -0.791  1.00  0.00           H  
HETATM   39  H6  UNL     1       0.015  -1.475   1.970  1.00  0.00           H  
HETATM   40  H7  UNL     1      -2.994  -1.026   1.891  1.00  0.00           H  
HETATM   41  H8  UNL     1      -2.314  -2.343   3.653  1.00  0.00           H  
HETATM   42  H9  UNL     1      -0.782  -1.436   3.958  1.00  0.00           H  
HETATM   43  H10 UNL     1      -2.356  -0.661   4.307  1.00  0.00           H  
HETATM   44  H11 UNL     1      -2.510   3.202   1.813  1.00  0.00           H  
HETATM   45  H12 UNL     1      -2.190   6.110   1.196  1.00  0.00           H  
HETATM   46  H13 UNL     1      -3.592   6.190   0.054  1.00  0.00           H  
HETATM   47  H14 UNL     1      -3.526   4.889   1.265  1.00  0.00           H  
HETATM   48  H15 UNL     1      -1.034   1.864  -3.765  1.00  0.00           H  
HETATM   49  H16 UNL     1      -0.299   3.383  -4.481  1.00  0.00           H  
HETATM   50  H17 UNL     1       0.589   2.361  -3.260  1.00  0.00           H  
HETATM   51  H18 UNL     1      -0.360   1.008  -2.010  1.00  0.00           H  
HETATM   52  H19 UNL     1      -0.985  -1.107  -0.799  1.00  0.00           H  
HETATM   53  H20 UNL     1       1.433  -0.032   1.934  1.00  0.00           H  
HETATM   54  H21 UNL     1       2.665   1.127   3.069  1.00  0.00           H  
HETATM   55  H22 UNL     1       3.131  -0.563   3.620  1.00  0.00           H  
HETATM   56  H23 UNL     1       4.280   0.884   3.747  1.00  0.00           H  
HETATM   57  H24 UNL     1       6.505   0.405  -1.849  1.00  0.00           H  
HETATM   58  H25 UNL     1       6.432   0.979  -0.168  1.00  0.00           H  
HETATM   59  H26 UNL     1       5.156   1.512  -1.370  1.00  0.00           H  
HETATM   60  H27 UNL     1       1.985  -0.529  -4.289  1.00  0.00           H  
HETATM   61  H28 UNL     1       1.807  -2.204  -3.523  1.00  0.00           H  
HETATM   62  H29 UNL     1       3.129  -1.884  -4.663  1.00  0.00           H  
HETATM   63  H30 UNL     1       0.813  -1.075  -2.143  1.00  0.00           H  
CONECT    1    2   34   35   36
CONECT    2    3   37   38
CONECT    3    4
CONECT    4    5    5    6
CONECT    6    7   21   39
CONECT    7    8    9   40
CONECT    8   41   42   43
CONECT    9   10   10   11
CONECT   11   12   12   20
CONECT   12   13   44
CONECT   13   14   16   16
CONECT   14   15
CONECT   15   45   46   47
CONECT   16   17   19
CONECT   17   18
CONECT   18   48   49   50
CONECT   19   20   20   51
CONECT   20   21
CONECT   21   22   52
CONECT   22   23   23   33
CONECT   23   24   53
CONECT   24   25   27   27
CONECT   25   26
CONECT   26   54   55   56
CONECT   27   28   30
CONECT   28   29
CONECT   29   57   58   59
CONECT   30   31   33   33
CONECT   31   32
CONECT   32   60   61   62
CONECT   33   63
END
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SMILES for HMDB0254088 (Lignan)

CCOC(=O)C1C(C)C(=O)C2=CC(OC)=C(OC)C=C2C1C1=CC(OC)=C(OC)C(OC)=C1
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INCHI for HMDB0254088 (Lignan)

InChI=1S/C25H30O8/c1-8-33-25(27)21-13(2)23(26)16-12-18(29-4)17(28-3)11-15(16)22(21)14-9-19(30-5)24(32-7)20(10-14)31-6/h9-13,21-22H,8H2,1-7H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
LignansMeSH
NeolignanMeSH
NeolignansMeSH
Chemical FormulaC25H30O8
Average Molecular Weight458.507
Monoisotopic Molecular Weight458.194067926
IUPAC Nameethyl 6,7-dimethoxy-3-methyl-4-oxo-1-(3,4,5-trimethoxyphenyl)-1,2,3,4-tetrahydronaphthalene-2-carboxylate
Traditional Namelignan
CAS Registry NumberNot Available
SMILES
CCOC(=O)C1C(C)C(=O)C2=CC(OC)=C(OC)C=C2C1C1=CC(OC)=C(OC)C(OC)=C1
InChI Identifier
InChI=1S/C25H30O8/c1-8-33-25(27)21-13(2)23(26)16-12-18(29-4)17(28-3)11-15(16)22(21)14-9-19(30-5)24(32-7)20(10-14)31-6/h9-13,21-22H,8H2,1-7H3
InChI KeyPEIBIXYUYBVLDS-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as aryltetralin lignans. These are lignans with a structure based on the 1-phenyltetralin skeleton.
KingdomOrganic compounds
Super ClassLignans, neolignans and related compounds
ClassAryltetralin lignans
Sub ClassNot Available
Direct ParentAryltetralin lignans
Alternative Parents
Substituents
  • 1-aryltetralin lignan
  • 2-naphthalenecarboxylic acid
  • 2-naphthalenecarboxylic acid or derivatives
  • Tetralin
  • Phenoxy compound
  • Anisole
  • Methoxybenzene
  • Aryl alkyl ketone
  • Aryl ketone
  • Phenol ether
  • Alkyl aryl ether
  • Monocyclic benzene moiety
  • Benzenoid
  • Carboxylic acid ester
  • Ketone
  • Ether
  • Carboxylic acid derivative
  • Monocarboxylic acid or derivatives
  • Organic oxide
  • Organic oxygen compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aromatic homopolycyclic compound
Molecular FrameworkAromatic homopolycyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP3.9ALOGPS
logP3.18ChemAxon
logS-5ALOGPS
pKa (Strongest Acidic)13.42ChemAxon
pKa (Strongest Basic)-4.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area89.52 ŲChemAxon
Rotatable Bond Count9ChemAxon
Refractivity121.62 m³·mol⁻¹ChemAxon
Polarizability48.7 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+210.15530932474
DeepCCS[M-H]-207.7630932474
DeepCCS[M-2H]-240.64330932474
DeepCCS[M+Na]+216.06830932474
AllCCS[M+H]+208.532859911
AllCCS[M+H-H2O]+206.232859911
AllCCS[M+NH4]+210.632859911
AllCCS[M+Na]+211.232859911
AllCCS[M-H]-215.732859911
AllCCS[M+Na-2H]-216.532859911
AllCCS[M+HCOO]-217.532859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
LignanCCOC(=O)C1C(C)C(=O)C2=CC(OC)=C(OC)C=C2C1C1=CC(OC)=C(OC)C(OC)=C14951.9Standard polar33892256
LignanCCOC(=O)C1C(C)C(=O)C2=CC(OC)=C(OC)C=C2C1C1=CC(OC)=C(OC)C(OC)=C13466.8Standard non polar33892256
LignanCCOC(=O)C1C(C)C(=O)C2=CC(OC)=C(OC)C=C2C1C1=CC(OC)=C(OC)C(OC)=C13275.7Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Lignan GC-MS (Non-derivatized) - 70eV, Positivesplash10-002u-4019700000-91aaf031b903452491ac2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Lignan GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lignan 10V, Positive-QTOFsplash10-03dr-0003900000-49350eac98068469f5842021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lignan 20V, Positive-QTOFsplash10-03dj-0027900000-c0556fb4d168b0f7f8ea2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lignan 40V, Positive-QTOFsplash10-014j-0092000000-ffda4b9ae1eab4421c982021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lignan 10V, Negative-QTOFsplash10-0a4i-0000900000-f001388b5341ed12f0982021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lignan 20V, Negative-QTOFsplash10-0a4i-0004900000-bcd871e8744793a433eb2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lignan 40V, Negative-QTOFsplash10-014i-0019200000-446d19a70e8460fbca9c2021-10-12Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDC00000702
Chemspider ID229263
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkLignan
METLIN IDNot Available
PubChem Compound261166
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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 ]

Enzymes

Enzyme Details
1. Phenylcoumaran benzylic ether reductase Pyrc5
General function:
Not Available
Specific function:
Oxidoreductase involved in lignan biosynthesis (PubMed:11606193). Catalyzes the NADPH-dependent reduction of phenylcoumaran benzylic ethers (PubMed:11606193). Converts dehydrodiconiferyl alcohol (DDC) to isodihydrodehydrodiconiferyl alcohol (IDDDC) (PubMed:11606193).
Gene Name:
PYRC5
Uniprot ID:
O81355
Molecular weight:
33822.305
Enzyme Details
2. Secoisolariciresinol dehydrogenase
General function:
Not Available
Specific function:
Oxidoreductase involved in lignan biosynthesis. Catalyzes the stereospecific conversion of (-)-secoisolariciresinol to (-)-matairesinol via a lactol intermediate.
Gene Name:
Not Available
Uniprot ID:
Q94KL7
Molecular weight:
29255.86
Enzyme Details
3. Secoisolariciresinol dehydrogenase
General function:
Not Available
Specific function:
Oxidoreductase involved in lignan biosynthesis. Catalyzes the stereospecific conversion of (-)-secoisolariciresinol to (-)-matairesinol via a lactol intermediate.
Gene Name:
(KEGG) SECOISOLARICIRESINOL DEHYDROGENASE (EC:1.1.1.331)
Uniprot ID:
Q94KL8
Molecular weight:
29252.965
Enzyme Details
4. Phenylcoumaran benzylic ether reductase Betv6
General function:
Not Available
Specific function:
Oxidoreductase involved in lignan biosynthesis (PubMed:11606193). Catalyzes the NADPH-dependent reduction of phenylcoumaran benzylic ethers (PubMed:11606193). Converts dehydrodiconiferyl alcohol (DDC) to isodihydrodehydrodiconiferyl alcohol (IDDDC) (PubMed:11606193).
Gene Name:
BETV6
Uniprot ID:
Q9FUW6
Molecular weight:
34190.045