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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 01:13:46 UTC

Update Date

2021-09-26 22:58:08 UTC

HMDB ID

HMDB0248058

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Agathic acid

Description

Agathic acid, also known as agathate, belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. Based on a literature review very few articles have been published on Agathic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). Agathic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Agathic acid 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

HMDB0248058
     RDKit          3D
Agathic acid
 54 55  0  0  0  0  0  0  0  0999 V2000
    1.4214   -2.7222    0.3637 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3181   -2.1436   -0.0564 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9495   -2.9106   -0.0413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1158   -2.0507    0.3797 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9998   -0.6974   -0.3610 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2630    0.0430   -0.3088 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3440   -0.7048    0.4714 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8568    0.2146   -1.6853 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2452   -0.2656   -2.6757 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0380    0.8730   -1.9071 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2020    1.4127    0.2994 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9944    2.1872   -0.1138 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7065    1.4338   -0.1288 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7481   -0.0201    0.1412 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6333   -0.3104    1.6374 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4009   -0.7111   -0.5419 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7651   -0.2137   -0.4202 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1822    1.1306   -0.8443 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7049    1.1656   -0.5986 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1764    1.0054    0.7804 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5136    1.3544   -1.5955 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9511    1.3899   -1.3894 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6781    1.5857   -2.4284 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5610    1.2247   -0.1484 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4012   -2.2928    0.4087 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3258   -3.7779    0.7119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8629   -3.7524    0.6743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1041   -3.3239   -1.0566 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2192   -1.9258    1.4545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0313   -2.5393   -0.0126 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8058   -1.0008   -1.4191 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0283   -0.9846    1.4749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7934   -1.5210   -0.1253 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1757    0.0494    0.5962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6634    1.1124   -1.1638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0936    1.9743   -0.0544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3022    1.3594    1.4033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1468    2.6254   -1.1369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9218    3.0720    0.5493 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0844    1.8741    0.7205 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2041    1.5896   -1.0979 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2905   -1.3424    1.7687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5731   -0.1233    2.1548 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1356    0.3494    2.0889 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1046   -0.7501   -1.6339 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1963   -0.3574    0.6172 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4197   -0.9348   -1.0323 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8662    1.9958   -0.2355 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0180    1.3804   -1.9132 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8014    0.0978    0.8902 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3226    0.9978    1.5206 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7782    1.9086    1.1086 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0935    1.4871   -2.5987 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2612    0.4824   -0.1018 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
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  8 10  1  0
  6 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 19 21  2  3
 21 22  1  0
 22 23  2  0
 22 24  1  0
 16  2  1  0
 14  5  1  0
  1 25  1  0
  1 26  1  0
  3 27  1  0
  3 28  1  0
  4 29  1  0
  4 30  1  0
  5 31  1  0
  7 32  1  0
  7 33  1  0
  7 34  1  0
 10 35  1  0
 11 36  1  0
 11 37  1  0
 12 38  1  0
 12 39  1  0
 13 40  1  0
 13 41  1  0
 15 42  1  0
 15 43  1  0
 15 44  1  0
 16 45  1  0
 17 46  1  0
 17 47  1  0
 18 48  1  0
 18 49  1  0
 20 50  1  0
 20 51  1  0
 20 52  1  0
 21 53  1  0
 24 54  1  0
M  END


  Mrv1533004161506252D          

 24 25  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    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    3.7125    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    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
   -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
   -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
    0.7145    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
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8163   -2.3784    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0416   -2.3784    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4788   -3.0781    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2171   -2.4072    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  4  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
  9 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 14 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0248058

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(CCC1C(=C)CCC2C1(C)CCCC2(C)C(O)=O)=CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H30O4/c1-13(12-17(21)22)6-8-15-14(2)7-9-16-19(15,3)10-5-11-20(16,4)18(23)24/h12,15-16H,2,5-11H2,1,3-4H3,(H,21,22)(H,23,24)

> <INCHI_KEY>
QYCOHMYDSOZCQD-UHFFFAOYSA-N

> <FORMULA>
C20H30O4

> <MOLECULAR_WEIGHT>
334.456

> <EXACT_MASS>
334.214409446

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
54

> <JCHEM_AVERAGE_POLARIZABILITY>
37.49758958828303

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-(4-carboxy-3-methylbut-3-en-1-yl)-1,4a-dimethyl-6-methylidene-decahydronaphthalene-1-carboxylic acid

> <ALOGPS_LOGP>
3.88

> <JCHEM_LOGP>
4.671277583333334

> <ALOGPS_LOGS>
-4.34

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.175528929748271

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.5724332023814025

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
93.63839999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.54e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-(4-carboxy-3-methylbut-3-en-1-yl)-1,4a-dimethyl-6-methylidene-hexahydro-2H-naphthalene-1-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0248058
     RDKit          3D
Agathic acid
 54 55  0  0  0  0  0  0  0  0999 V2000
    1.4214   -2.7222    0.3637 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3181   -2.1436   -0.0564 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9495   -2.9106   -0.0413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1158   -2.0507    0.3797 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9998   -0.6974   -0.3610 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2630    0.0430   -0.3088 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3440   -0.7048    0.4714 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8568    0.2146   -1.6853 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2452   -0.2656   -2.6757 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0380    0.8730   -1.9071 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2020    1.4127    0.2994 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9944    2.1872   -0.1138 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7065    1.4338   -0.1288 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7481   -0.0201    0.1412 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6333   -0.3104    1.6374 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4009   -0.7111   -0.5419 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7651   -0.2137   -0.4202 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1822    1.1306   -0.8443 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7049    1.1656   -0.5986 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1764    1.0054    0.7804 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5136    1.3544   -1.5955 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9511    1.3899   -1.3894 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6781    1.5857   -2.4284 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5610    1.2247   -0.1484 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4012   -2.2928    0.4087 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3258   -3.7779    0.7119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8629   -3.7524    0.6743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1041   -3.3239   -1.0566 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2192   -1.9258    1.4545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0313   -2.5393   -0.0126 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8058   -1.0008   -1.4191 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0283   -0.9846    1.4749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7934   -1.5210   -0.1253 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1757    0.0494    0.5962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6634    1.1124   -1.1638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0936    1.9743   -0.0544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3022    1.3594    1.4033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1468    2.6254   -1.1369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9218    3.0720    0.5493 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0844    1.8741    0.7205 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2041    1.5896   -1.0979 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2905   -1.3424    1.7687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5731   -0.1233    2.1548 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1356    0.3494    2.0889 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1046   -0.7501   -1.6339 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1963   -0.3574    0.6172 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4197   -0.9348   -1.0323 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8662    1.9958   -0.2355 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0180    1.3804   -1.9132 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8014    0.0978    0.8902 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3226    0.9978    1.5206 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7782    1.9086    1.1086 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0935    1.4871   -2.5987 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2612    0.4824   -0.1018 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
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  8 10  1  0
  6 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 19 21  2  3
 21 22  1  0
 22 23  2  0
 22 24  1  0
 16  2  1  0
 14  5  1  0
  1 25  1  0
  1 26  1  0
  3 27  1  0
  3 28  1  0
  4 29  1  0
  4 30  1  0
  5 31  1  0
  7 32  1  0
  7 33  1  0
  7 34  1  0
 10 35  1  0
 11 36  1  0
 11 37  1  0
 12 38  1  0
 12 39  1  0
 13 40  1  0
 13 41  1  0
 15 42  1  0
 15 43  1  0
 15 44  1  0
 16 45  1  0
 17 46  1  0
 17 47  1  0
 18 48  1  0
 18 49  1  0
 20 50  1  0
 20 51  1  0
 20 52  1  0
 21 53  1  0
 24 54  1  0
M  END

HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         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   3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.334   6.930   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      -1.334   6.930   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.334   0.770   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.390  -4.440   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.944  -4.440   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       2.760  -5.746   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       0.405  -4.493   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    2    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   15                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   20                                                  
CONECT   15   14    9   16   17                                             
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   14   21   22                                             
CONECT   21   20                                                            
CONECT   22   20   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   50    0
END

COMPND    HMDB0248058
HETATM    1  C1  UNL     1       1.421  -2.722   0.364  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.318  -2.144  -0.056  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.950  -2.911  -0.041  1.00  0.00           C  
HETATM    4  C4  UNL     1      -2.116  -2.051   0.380  1.00  0.00           C  
HETATM    5  C5  UNL     1      -2.000  -0.697  -0.361  1.00  0.00           C  
HETATM    6  C6  UNL     1      -3.263   0.043  -0.309  1.00  0.00           C  
HETATM    7  C7  UNL     1      -4.344  -0.705   0.471  1.00  0.00           C  
HETATM    8  C8  UNL     1      -3.857   0.215  -1.685  1.00  0.00           C  
HETATM    9  O1  UNL     1      -3.245  -0.266  -2.676  1.00  0.00           O  
HETATM   10  O2  UNL     1      -5.038   0.873  -1.907  1.00  0.00           O  
HETATM   11  C9  UNL     1      -3.202   1.413   0.299  1.00  0.00           C  
HETATM   12  C10 UNL     1      -1.994   2.187  -0.114  1.00  0.00           C  
HETATM   13  C11 UNL     1      -0.707   1.434  -0.129  1.00  0.00           C  
HETATM   14  C12 UNL     1      -0.748  -0.020   0.141  1.00  0.00           C  
HETATM   15  C13 UNL     1      -0.633  -0.310   1.637  1.00  0.00           C  
HETATM   16  C14 UNL     1       0.401  -0.711  -0.542  1.00  0.00           C  
HETATM   17  C15 UNL     1       1.765  -0.214  -0.420  1.00  0.00           C  
HETATM   18  C16 UNL     1       2.182   1.131  -0.844  1.00  0.00           C  
HETATM   19  C17 UNL     1       3.705   1.166  -0.599  1.00  0.00           C  
HETATM   20  C18 UNL     1       4.176   1.005   0.780  1.00  0.00           C  
HETATM   21  C19 UNL     1       4.514   1.354  -1.596  1.00  0.00           C  
HETATM   22  C20 UNL     1       5.951   1.390  -1.389  1.00  0.00           C  
HETATM   23  O3  UNL     1       6.678   1.586  -2.428  1.00  0.00           O  
HETATM   24  O4  UNL     1       6.561   1.225  -0.148  1.00  0.00           O  
HETATM   25  H1  UNL     1       2.401  -2.293   0.409  1.00  0.00           H  
HETATM   26  H2  UNL     1       1.326  -3.778   0.712  1.00  0.00           H  
HETATM   27  H3  UNL     1      -0.863  -3.752   0.674  1.00  0.00           H  
HETATM   28  H4  UNL     1      -1.104  -3.324  -1.057  1.00  0.00           H  
HETATM   29  H5  UNL     1      -2.219  -1.926   1.455  1.00  0.00           H  
HETATM   30  H6  UNL     1      -3.031  -2.539  -0.013  1.00  0.00           H  
HETATM   31  H7  UNL     1      -1.806  -1.001  -1.419  1.00  0.00           H  
HETATM   32  H8  UNL     1      -4.028  -0.985   1.475  1.00  0.00           H  
HETATM   33  H9  UNL     1      -4.793  -1.521  -0.125  1.00  0.00           H  
HETATM   34  H10 UNL     1      -5.176   0.049   0.596  1.00  0.00           H  
HETATM   35  H11 UNL     1      -5.663   1.112  -1.164  1.00  0.00           H  
HETATM   36  H12 UNL     1      -4.094   1.974  -0.054  1.00  0.00           H  
HETATM   37  H13 UNL     1      -3.302   1.359   1.403  1.00  0.00           H  
HETATM   38  H14 UNL     1      -2.147   2.625  -1.137  1.00  0.00           H  
HETATM   39  H15 UNL     1      -1.922   3.072   0.549  1.00  0.00           H  
HETATM   40  H16 UNL     1      -0.084   1.874   0.720  1.00  0.00           H  
HETATM   41  H17 UNL     1      -0.204   1.590  -1.098  1.00  0.00           H  
HETATM   42  H18 UNL     1      -0.290  -1.342   1.769  1.00  0.00           H  
HETATM   43  H19 UNL     1      -1.573  -0.123   2.155  1.00  0.00           H  
HETATM   44  H20 UNL     1       0.136   0.349   2.089  1.00  0.00           H  
HETATM   45  H21 UNL     1       0.105  -0.750  -1.634  1.00  0.00           H  
HETATM   46  H22 UNL     1       2.196  -0.357   0.617  1.00  0.00           H  
HETATM   47  H23 UNL     1       2.420  -0.935  -1.032  1.00  0.00           H  
HETATM   48  H24 UNL     1       1.866   1.996  -0.235  1.00  0.00           H  
HETATM   49  H25 UNL     1       2.018   1.380  -1.913  1.00  0.00           H  
HETATM   50  H26 UNL     1       4.801   0.098   0.890  1.00  0.00           H  
HETATM   51  H27 UNL     1       3.323   0.998   1.521  1.00  0.00           H  
HETATM   52  H28 UNL     1       4.778   1.909   1.109  1.00  0.00           H  
HETATM   53  H29 UNL     1       4.093   1.487  -2.599  1.00  0.00           H  
HETATM   54  H30 UNL     1       7.261   0.482  -0.102  1.00  0.00           H  
CONECT    1    2    2   25   26
CONECT    2    3   16
CONECT    3    4   27   28
CONECT    4    5   29   30
CONECT    5    6   14   31
CONECT    6    7    8   11
CONECT    7   32   33   34
CONECT    8    9    9   10
CONECT   10   35
CONECT   11   12   36   37
CONECT   12   13   38   39
CONECT   13   14   40   41
CONECT   14   15   16
CONECT   15   42   43   44
CONECT   16   17   45
CONECT   17   18   46   47
CONECT   18   19   48   49
CONECT   19   20   21   21
CONECT   20   50   51   52
CONECT   21   22   53
CONECT   22   23   23   24
CONECT   24   54
END

HMDB0248058
     RDKit          3D
Agathic acid
 54 55  0  0  0  0  0  0  0  0999 V2000
    1.4214   -2.7222    0.3637 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3181   -2.1436   -0.0564 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9495   -2.9106   -0.0413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1158   -2.0507    0.3797 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9998   -0.6974   -0.3610 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2630    0.0430   -0.3088 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3440   -0.7048    0.4714 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8568    0.2146   -1.6853 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2452   -0.2656   -2.6757 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0380    0.8730   -1.9071 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2020    1.4127    0.2994 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9944    2.1872   -0.1138 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7065    1.4338   -0.1288 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7481   -0.0201    0.1412 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6333   -0.3104    1.6374 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4009   -0.7111   -0.5419 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7651   -0.2137   -0.4202 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1822    1.1306   -0.8443 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7049    1.1656   -0.5986 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1764    1.0054    0.7804 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5136    1.3544   -1.5955 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9511    1.3899   -1.3894 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6781    1.5857   -2.4284 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5610    1.2247   -0.1484 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4012   -2.2928    0.4087 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3258   -3.7779    0.7119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8629   -3.7524    0.6743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1041   -3.3239   -1.0566 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2192   -1.9258    1.4545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0313   -2.5393   -0.0126 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8058   -1.0008   -1.4191 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0283   -0.9846    1.4749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7934   -1.5210   -0.1253 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1757    0.0494    0.5962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6634    1.1124   -1.1638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0936    1.9743   -0.0544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3022    1.3594    1.4033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1468    2.6254   -1.1369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9218    3.0720    0.5493 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0844    1.8741    0.7205 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2041    1.5896   -1.0979 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2905   -1.3424    1.7687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5731   -0.1233    2.1548 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1356    0.3494    2.0889 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1046   -0.7501   -1.6339 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1963   -0.3574    0.6172 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4197   -0.9348   -1.0323 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8662    1.9958   -0.2355 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0180    1.3804   -1.9132 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8014    0.0978    0.8902 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3226    0.9978    1.5206 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7782    1.9086    1.1086 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0935    1.4871   -2.5987 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2612    0.4824   -0.1018 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
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  8 10  1  0
  6 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 19 21  2  3
 21 22  1  0
 22 23  2  0
 22 24  1  0
 16  2  1  0
 14  5  1  0
  1 25  1  0
  1 26  1  0
  3 27  1  0
  3 28  1  0
  4 29  1  0
  4 30  1  0
  5 31  1  0
  7 32  1  0
  7 33  1  0
  7 34  1  0
 10 35  1  0
 11 36  1  0
 11 37  1  0
 12 38  1  0
 12 39  1  0
 13 40  1  0
 13 41  1  0
 15 42  1  0
 15 43  1  0
 15 44  1  0
 16 45  1  0
 17 46  1  0
 17 47  1  0
 18 48  1  0
 18 49  1  0
 20 50  1  0
 20 51  1  0
 20 52  1  0
 21 53  1  0
 24 54  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Agathate	Generator

Chemical Formula

C₂₀H₃₀O₄

Average Molecular Weight

334.456

Monoisotopic Molecular Weight

334.214409446

IUPAC Name

5-(4-carboxy-3-methylbut-3-en-1-yl)-1,4a-dimethyl-6-methylidene-decahydronaphthalene-1-carboxylic acid

Traditional Name

5-(4-carboxy-3-methylbut-3-en-1-yl)-1,4a-dimethyl-6-methylidene-hexahydro-2H-naphthalene-1-carboxylic acid

CAS Registry Number

Not Available

SMILES

CC(CCC1C(=C)CCC2C1(C)CCCC2(C)C(O)=O)=CC(O)=O

InChI Identifier

InChI=1S/C20H30O4/c1-13(12-17(21)22)6-8-15-14(2)7-9-16-19(15,3)10-5-11-20(16,4)18(23)24/h12,15-16H,2,5-11H2,1,3-4H3,(H,21,22)(H,23,24)

InChI Key

QYCOHMYDSOZCQD-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Diterpenoids

Alternative Parents

Substituents

Labdane diterpenoid
Diterpenoid
Medium-chain fatty acid
Branched fatty acid
Methyl-branched fatty acid
Dicarboxylic acid or derivatives
Fatty acyl
Fatty acid
Unsaturated fatty acid
Carboxylic acid derivative
Carboxylic acid
Organic oxide
Organic oxygen compound
Carbonyl group
Hydrocarbon derivative
Organooxygen compound
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

Not Available

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	3.88	ALOGPS
logP	4.67	ChemAxon
logS	-4.3	ALOGPS
pKa (Strongest Acidic)	4.57	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	74.6 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	93.64 m³·mol⁻¹	ChemAxon
Polarizability	37.5 Å³	ChemAxon
Number of Rings	2	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]+	182.669	30932474
DeepCCS	[M-H]-	180.311	30932474
DeepCCS	[M-2H]-	213.197	30932474
DeepCCS	[M+Na]+	188.762	30932474

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Agathic acid	CC(CCC1C(=C)CCC2C1(C)CCCC2(C)C(O)=O)=CC(O)=O	3861.9	Standard polar	33892256
Agathic acid	CC(CCC1C(=C)CCC2C1(C)CCCC2(C)C(O)=O)=CC(O)=O	2397.3	Standard non polar	33892256
Agathic acid	CC(CCC1C(=C)CCC2C1(C)CCCC2(C)C(O)=O)=CC(O)=O	2691.1	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 - Agathic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-014r-2293000000-145dcb5b4c3c87e10356	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Agathic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Agathic acid GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Agathic acid GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Agathic acid GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Agathic acid GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Agathic acid GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Agathic acid GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agathic acid 10V, Positive-QTOF	splash10-000i-0193000000-f218c5ce661dd8ca64e1	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agathic acid 20V, Positive-QTOF	splash10-000i-1960000000-46cb64c934a1fe2ad499	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agathic acid 40V, Positive-QTOF	splash10-066r-9530000000-ab782c40c921566340b0	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agathic acid 10V, Negative-QTOF	splash10-000i-0091000000-cbb5c6914849c88c5608	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agathic acid 20V, Negative-QTOF	splash10-000i-1091000000-7fd4454cd742ea21a3ee	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Agathic acid 40V, Negative-QTOF	splash10-000w-3091000000-872dcbe11546429dbbcd	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

C00041322

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

541901

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

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 Agathic acid (HMDB0248058)

MOL for HMDB0248058 (Agathic acid)

3D MOL for HMDB0248058 (Agathic acid)

3D SDF for HMDB0248058 (Agathic acid)

3D-SDF for HMDB0248058 (Agathic acid)

PDB for HMDB0248058 (Agathic acid)

3D PDB for HMDB0248058 (Agathic acid)

SMILES for HMDB0248058 (Agathic acid)

INCHI for HMDB0248058 (Agathic acid)

Structure for HMDB0248058 (Agathic acid)

3D Structure for HMDB0248058 (Agathic acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra