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Showing metabocard for Hederagenin (HMDB0253065)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 11:14:14 UTC
Update Date2021-09-26 23:06:03 UTC
HMDB IDHMDB0253065
Secondary Accession NumbersNone
Metabolite Identification
Common NameHederagenin
Descriptionhederagenin belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Based on a literature review very few articles have been published on hederagenin. This compound has been identified in human blood as reported by (PMID: 31557052 ). Hederagenin is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Hederagenin 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 HMDB0253065 (Hederagenin)


  Mrv1533004171501022D          

 34 38  0  0  0  0            999 V2000
    0.4452   -3.0106    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -3.8230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.1105   -4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -5.2520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -5.2520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -5.9664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -5.9664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.1895   -5.9664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D MOL for HMDB0253065 (Hederagenin)

HMDB0253065
     RDKit          3D
Hederagenin
 82 86  0  0  0  0  0  0  0  0999 V2000
   -6.3800    0.8286    0.9148 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.5493    0.2752    2.3990 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.5125   -0.5167   -2.1797 C   0  0  0  0  0  0  0  0  0  0  0  0
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 33 80  1  0
 34 81  1  0
 34 82  1  0
M  END
Download

3D SDF for HMDB0253065 (Hederagenin)


  Mrv1533004171501022D          

 34 38  0  0  0  0            999 V2000
    0.4452   -3.0106    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -3.8230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4733   -3.5409    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1105   -4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -5.2520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.5395   -5.9664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.9337   -6.0644    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.1105   -5.9664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -6.6809    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
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  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
  9 11  1  0  0  0  0
 11 12  2  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
 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
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 21 25  1  0  0  0  0
 15 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
  9 28  1  0  0  0  0
 14 28  1  0  0  0  0
 28 29  1  0  0  0  0
 11 30  1  0  0  0  0
  6 30  1  0  0  0  0
 30 31  1  0  0  0  0
  2 31  1  0  0  0  0
  6 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0253065

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1(C)CCC2(CCC3(C)C(=CCC4C5(C)CCC(O)C(C)(CO)C5CCC34C)C2C1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C30H48O4/c1-25(2)13-15-30(24(33)34)16-14-28(5)19(20(30)17-25)7-8-22-26(3)11-10-23(32)27(4,18-31)21(26)9-12-29(22,28)6/h7,20-23,31-32H,8-18H2,1-6H3,(H,33,34)

> <INCHI_KEY>
PGOYMURMZNDHNS-UHFFFAOYSA-N

> <FORMULA>
C30H48O4

> <MOLECULAR_WEIGHT>
472.71

> <EXACT_MASS>
472.355260026

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
82

> <JCHEM_AVERAGE_POLARIZABILITY>
55.920061669320944

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
10-hydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,12b,13,14b-icosahydropicene-4a-carboxylic acid

> <ALOGPS_LOGP>
6.17

> <JCHEM_LOGP>
5.314062276666666

> <ALOGPS_LOGS>
-5.15

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.485961383006249

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.744259192501462

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7854425934406057

> <JCHEM_POLAR_SURFACE_AREA>
77.76

> <JCHEM_REFRACTIVITY>
135.3992

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.38e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
10-hydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0253065 (Hederagenin)

HMDB0253065
     RDKit          3D
Hederagenin
 82 86  0  0  0  0  0  0  0  0999 V2000
   -6.3800    0.8286    0.9148 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9494    0.2612    0.9327 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5493    0.2752    2.3990 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0190   -1.1661    0.5043 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7623   -1.6747   -0.1484 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3335   -0.7649   -1.2762 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5125   -0.5167   -2.1797 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8450    0.6339   -2.4459 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1805   -1.6021   -2.6809 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2735   -1.3300   -2.1444 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9572   -0.6004   -2.1145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5158   -0.3010   -0.7292 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2251   -1.6243   -0.0641 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6069    0.3968    0.0079 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2155    0.9092    1.1801 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1504    0.8345    1.7478 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2083    0.4825    0.7409 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5630    1.0418    1.0264 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3927    2.4618    1.5151 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0846    0.3340    2.2763 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3771   -1.1060    2.0776 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9816   -1.4315    0.7493 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0501   -2.3024    0.9650 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5585   -0.1900    0.1103 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7256    0.2728    0.9883 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1809   -0.6657   -1.1871 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1676   -1.6057   -0.7857 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5519    0.9204   -0.0837 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9488    0.9380   -1.4593 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6908    0.1561   -1.6150 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6739    0.6420   -0.6268 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2355    2.0096   -1.0100 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9284    0.5194   -0.5969 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0078    1.1382    0.2024 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8696    0.7322    1.8884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0105    0.2753    0.1775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3568    1.9259    0.6783 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3755   -0.2093    2.9560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5048    1.3238    2.7687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6184   -0.2866    2.5844 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8372   -1.2891   -0.2358 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2561   -1.8606    1.3370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8823   -2.7077   -0.5165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9588   -1.6773    0.6074 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7152   -2.4297   -3.0563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2022   -2.4216   -1.9601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5636   -1.3008   -3.2494 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0007    0.2337   -2.8088 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2018   -1.3210   -2.5501 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9493   -2.4111   -0.4431 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7604   -2.0677   -0.3734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3999   -1.6393    1.0247 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9829    1.4096    1.7394 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3265    1.8518    2.1916 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1185    0.0667    2.5619 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3375   -0.6467    0.8704 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1852    2.4855    2.6222 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7080    3.0823    0.9512 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3847    3.0169    1.4651 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8964    0.9143    2.7621 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2238    0.3980    3.0085 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4541   -1.7196    2.1946 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0415   -1.4289    2.9196 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2802   -1.9633    0.0697 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9541   -3.1577    0.4814 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7712   -0.3244    1.9236 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6559    1.3602    1.1934 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7108    0.1259    0.4957 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7079    0.1030   -1.7455 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4864   -1.3003   -1.7825 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0693   -1.2785   -0.9401 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1853    1.8601   -0.0373 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6613    0.4825   -2.2123 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8719    1.9886   -1.8641 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8997   -0.9105   -1.5870 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2898    0.3795   -2.6277 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2811    2.5974   -0.2306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3651    1.9525   -1.9523 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0765    2.6984   -1.3197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7623    1.1994   -1.5117 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5795    1.9607    0.8312 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6628    1.7527   -0.5025 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  6 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 18 20  1  0
 20 21  1  0
 21 22  1  0
 22 23  1  0
 22 24  1  0
 24 25  1  0
 24 26  1  0
 26 27  1  0
 24 28  1  0
 28 29  1  0
 29 30  1  0
 30 31  1  0
 31 32  1  0
 14 33  1  0
 33 34  1  0
 34  2  1  0
 33  6  1  0
 31 12  1  0
 31 17  1  0
 28 18  1  0
  1 35  1  0
  1 36  1  0
  1 37  1  0
  3 38  1  0
  3 39  1  0
  3 40  1  0
  4 41  1  0
  4 42  1  0
  5 43  1  0
  5 44  1  0
  9 45  1  0
 10 46  1  0
 10 47  1  0
 11 48  1  0
 11 49  1  0
 13 50  1  0
 13 51  1  0
 13 52  1  0
 15 53  1  0
 16 54  1  0
 16 55  1  0
 17 56  1  0
 19 57  1  0
 19 58  1  0
 19 59  1  0
 20 60  1  0
 20 61  1  0
 21 62  1  0
 21 63  1  0
 22 64  1  0
 23 65  1  0
 25 66  1  0
 25 67  1  0
 25 68  1  0
 26 69  1  0
 26 70  1  0
 27 71  1  0
 28 72  1  0
 29 73  1  0
 29 74  1  0
 30 75  1  0
 30 76  1  0
 32 77  1  0
 32 78  1  0
 32 79  1  0
 33 80  1  0
 34 81  1  0
 34 82  1  0
M  END
Download

PDB for HMDB0253065 (Hederagenin)

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0       0.831  -5.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.564  -7.136   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.883  -6.610   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.206  -8.470   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.564  -9.804   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.104  -9.804   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.874 -11.137   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.414 -11.137   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.184  -9.804   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.954 -11.137   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.414  -8.470   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.184  -7.136   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.724  -7.136   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.494  -8.470   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.034  -8.470   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.264  -7.136   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.804  -7.136   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      11.344  -7.136   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      12.114  -8.470   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      13.654  -8.470   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      11.344  -9.804   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      11.076 -11.320   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      12.791 -10.330   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      13.058 -11.847   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       9.804  -9.804   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       9.034 -11.137   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       7.494 -11.137   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       6.724  -9.804   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.885 -11.335   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.874  -8.470   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       2.104  -7.136   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       1.334 -11.137   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -0.206 -11.137   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       2.104 -12.471   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4   31                                             
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   30   32                                             
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11   28                                             
CONECT   10    9                                                            
CONECT   11    9   12   30                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   28                                                  
CONECT   15   14   16   17   25                                             
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   23   25                                             
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23                                                            
CONECT   25   21   15   26                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27    9   14   29                                             
CONECT   29   28                                                            
CONECT   30   11    6   31                                                  
CONECT   31   30    2                                                       
CONECT   32    6   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   76    0
END
Download

3D PDB for HMDB0253065 (Hederagenin)

COMPND    HMDB0253065
HETATM    1  C1  UNL     1      -6.380   0.829   0.915  1.00  0.00           C  
HETATM    2  C2  UNL     1      -4.949   0.261   0.933  1.00  0.00           C  
HETATM    3  C3  UNL     1      -4.549   0.275   2.399  1.00  0.00           C  
HETATM    4  C4  UNL     1      -5.019  -1.166   0.504  1.00  0.00           C  
HETATM    5  C5  UNL     1      -3.762  -1.675  -0.148  1.00  0.00           C  
HETATM    6  C6  UNL     1      -3.333  -0.765  -1.276  1.00  0.00           C  
HETATM    7  C7  UNL     1      -4.513  -0.517  -2.180  1.00  0.00           C  
HETATM    8  O1  UNL     1      -4.845   0.634  -2.446  1.00  0.00           O  
HETATM    9  O2  UNL     1      -5.180  -1.602  -2.681  1.00  0.00           O  
HETATM   10  C8  UNL     1      -2.274  -1.330  -2.144  1.00  0.00           C  
HETATM   11  C9  UNL     1      -0.957  -0.600  -2.115  1.00  0.00           C  
HETATM   12  C10 UNL     1      -0.516  -0.301  -0.729  1.00  0.00           C  
HETATM   13  C11 UNL     1      -0.225  -1.624  -0.064  1.00  0.00           C  
HETATM   14  C12 UNL     1      -1.607   0.397   0.008  1.00  0.00           C  
HETATM   15  C13 UNL     1      -1.216   0.909   1.180  1.00  0.00           C  
HETATM   16  C14 UNL     1       0.150   0.835   1.748  1.00  0.00           C  
HETATM   17  C15 UNL     1       1.208   0.483   0.741  1.00  0.00           C  
HETATM   18  C16 UNL     1       2.563   1.042   1.026  1.00  0.00           C  
HETATM   19  C17 UNL     1       2.393   2.462   1.515  1.00  0.00           C  
HETATM   20  C18 UNL     1       3.085   0.334   2.276  1.00  0.00           C  
HETATM   21  C19 UNL     1       3.377  -1.106   2.078  1.00  0.00           C  
HETATM   22  C20 UNL     1       3.982  -1.432   0.749  1.00  0.00           C  
HETATM   23  O3  UNL     1       5.050  -2.302   0.965  1.00  0.00           O  
HETATM   24  C21 UNL     1       4.559  -0.190   0.110  1.00  0.00           C  
HETATM   25  C22 UNL     1       5.726   0.273   0.988  1.00  0.00           C  
HETATM   26  C23 UNL     1       5.181  -0.666  -1.187  1.00  0.00           C  
HETATM   27  O4  UNL     1       6.168  -1.606  -0.786  1.00  0.00           O  
HETATM   28  C24 UNL     1       3.552   0.920  -0.084  1.00  0.00           C  
HETATM   29  C25 UNL     1       2.949   0.938  -1.459  1.00  0.00           C  
HETATM   30  C26 UNL     1       1.691   0.156  -1.615  1.00  0.00           C  
HETATM   31  C27 UNL     1       0.674   0.642  -0.627  1.00  0.00           C  
HETATM   32  C28 UNL     1       0.236   2.010  -1.010  1.00  0.00           C  
HETATM   33  C29 UNL     1      -2.928   0.519  -0.597  1.00  0.00           C  
HETATM   34  C30 UNL     1      -4.008   1.138   0.202  1.00  0.00           C  
HETATM   35  H1  UNL     1      -6.870   0.732   1.888  1.00  0.00           H  
HETATM   36  H2  UNL     1      -7.011   0.275   0.178  1.00  0.00           H  
HETATM   37  H3  UNL     1      -6.357   1.926   0.678  1.00  0.00           H  
HETATM   38  H4  UNL     1      -5.375  -0.209   2.956  1.00  0.00           H  
HETATM   39  H5  UNL     1      -4.505   1.324   2.769  1.00  0.00           H  
HETATM   40  H6  UNL     1      -3.618  -0.287   2.584  1.00  0.00           H  
HETATM   41  H7  UNL     1      -5.837  -1.289  -0.236  1.00  0.00           H  
HETATM   42  H8  UNL     1      -5.256  -1.861   1.337  1.00  0.00           H  
HETATM   43  H9  UNL     1      -3.882  -2.708  -0.517  1.00  0.00           H  
HETATM   44  H10 UNL     1      -2.959  -1.677   0.607  1.00  0.00           H  
HETATM   45  H11 UNL     1      -4.715  -2.430  -3.056  1.00  0.00           H  
HETATM   46  H12 UNL     1      -2.202  -2.422  -1.960  1.00  0.00           H  
HETATM   47  H13 UNL     1      -2.564  -1.301  -3.249  1.00  0.00           H  
HETATM   48  H14 UNL     1      -1.001   0.234  -2.809  1.00  0.00           H  
HETATM   49  H15 UNL     1      -0.202  -1.321  -2.550  1.00  0.00           H  
HETATM   50  H16 UNL     1      -0.949  -2.411  -0.443  1.00  0.00           H  
HETATM   51  H17 UNL     1       0.760  -2.068  -0.373  1.00  0.00           H  
HETATM   52  H18 UNL     1      -0.400  -1.639   1.025  1.00  0.00           H  
HETATM   53  H19 UNL     1      -1.983   1.410   1.739  1.00  0.00           H  
HETATM   54  H20 UNL     1       0.327   1.852   2.192  1.00  0.00           H  
HETATM   55  H21 UNL     1       0.118   0.067   2.562  1.00  0.00           H  
HETATM   56  H22 UNL     1       1.337  -0.647   0.870  1.00  0.00           H  
HETATM   57  H23 UNL     1       2.185   2.486   2.622  1.00  0.00           H  
HETATM   58  H24 UNL     1       1.708   3.082   0.951  1.00  0.00           H  
HETATM   59  H25 UNL     1       3.385   3.017   1.465  1.00  0.00           H  
HETATM   60  H26 UNL     1       3.896   0.914   2.762  1.00  0.00           H  
HETATM   61  H27 UNL     1       2.224   0.398   3.008  1.00  0.00           H  
HETATM   62  H28 UNL     1       2.454  -1.720   2.195  1.00  0.00           H  
HETATM   63  H29 UNL     1       4.041  -1.429   2.920  1.00  0.00           H  
HETATM   64  H30 UNL     1       3.280  -1.963   0.070  1.00  0.00           H  
HETATM   65  H31 UNL     1       4.954  -3.158   0.481  1.00  0.00           H  
HETATM   66  H32 UNL     1       5.771  -0.324   1.924  1.00  0.00           H  
HETATM   67  H33 UNL     1       5.656   1.360   1.193  1.00  0.00           H  
HETATM   68  H34 UNL     1       6.711   0.126   0.496  1.00  0.00           H  
HETATM   69  H35 UNL     1       5.708   0.103  -1.745  1.00  0.00           H  
HETATM   70  H36 UNL     1       4.486  -1.300  -1.783  1.00  0.00           H  
HETATM   71  H37 UNL     1       7.069  -1.279  -0.940  1.00  0.00           H  
HETATM   72  H38 UNL     1       4.185   1.860  -0.037  1.00  0.00           H  
HETATM   73  H39 UNL     1       3.661   0.482  -2.212  1.00  0.00           H  
HETATM   74  H40 UNL     1       2.872   1.989  -1.864  1.00  0.00           H  
HETATM   75  H41 UNL     1       1.900  -0.910  -1.587  1.00  0.00           H  
HETATM   76  H42 UNL     1       1.290   0.380  -2.628  1.00  0.00           H  
HETATM   77  H43 UNL     1      -0.281   2.597  -0.231  1.00  0.00           H  
HETATM   78  H44 UNL     1      -0.365   1.952  -1.952  1.00  0.00           H  
HETATM   79  H45 UNL     1       1.077   2.698  -1.320  1.00  0.00           H  
HETATM   80  H46 UNL     1      -2.762   1.199  -1.512  1.00  0.00           H  
HETATM   81  H47 UNL     1      -3.580   1.961   0.831  1.00  0.00           H  
HETATM   82  H48 UNL     1      -4.663   1.753  -0.502  1.00  0.00           H  
CONECT    1    2   35   36   37
CONECT    2    3    4   34
CONECT    3   38   39   40
CONECT    4    5   41   42
CONECT    5    6   43   44
CONECT    6    7   10   33
CONECT    7    8    8    9
CONECT    9   45
CONECT   10   11   46   47
CONECT   11   12   48   49
CONECT   12   13   14   31
CONECT   13   50   51   52
CONECT   14   15   15   33
CONECT   15   16   53
CONECT   16   17   54   55
CONECT   17   18   31   56
CONECT   18   19   20   28
CONECT   19   57   58   59
CONECT   20   21   60   61
CONECT   21   22   62   63
CONECT   22   23   24   64
CONECT   23   65
CONECT   24   25   26   28
CONECT   25   66   67   68
CONECT   26   27   69   70
CONECT   27   71
CONECT   28   29   72
CONECT   29   30   73   74
CONECT   30   31   75   76
CONECT   31   32
CONECT   32   77   78   79
CONECT   33   34   80
CONECT   34   81   82
END
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SMILES for HMDB0253065 (Hederagenin)

CC1(C)CCC2(CCC3(C)C(=CCC4C5(C)CCC(O)C(C)(CO)C5CCC34C)C2C1)C(O)=O
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INCHI for HMDB0253065 (Hederagenin)

InChI=1S/C30H48O4/c1-25(2)13-15-30(24(33)34)16-14-28(5)19(20(30)17-25)7-8-22-26(3)11-10-23(32)27(4,18-31)21(26)9-12-29(22,28)6/h7,20-23,31-32H,8-18H2,1-6H3,(H,33,34)
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC30H48O4
Average Molecular Weight472.71
Monoisotopic Molecular Weight472.355260026
IUPAC Name10-hydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,12b,13,14b-icosahydropicene-4a-carboxylic acid
Traditional Name10-hydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid
CAS Registry NumberNot Available
SMILES
CC1(C)CCC2(CCC3(C)C(=CCC4C5(C)CCC(O)C(C)(CO)C5CCC34C)C2C1)C(O)=O
InChI Identifier
InChI=1S/C30H48O4/c1-25(2)13-15-30(24(33)34)16-14-28(5)19(20(30)17-25)7-8-22-26(3)11-10-23(32)27(4,18-31)21(26)9-12-29(22,28)6/h7,20-23,31-32H,8-18H2,1-6H3,(H,33,34)
InChI KeyPGOYMURMZNDHNS-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassTriterpenoids
Direct ParentTriterpenoids
Alternative Parents
Substituents
  • Triterpenoid
  • Steroid
  • Cyclic alcohol
  • Secondary alcohol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic homopolycyclic compound
Molecular FrameworkAliphatic homopolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological location
ProcessNot Available
RoleNot 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
logP6.17ALOGPS
logP5.31ChemAxon
logS-5.2ALOGPS
pKa (Strongest Acidic)4.74ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area77.76 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity135.4 m³·mol⁻¹ChemAxon
Polarizability55.92 ųChemAxon
Number of Rings5ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M-2H]-247.76530932474
DeepCCS[M+Na]+223.00730932474
AllCCS[M+H]+216.432859911
AllCCS[M+H-H2O]+214.832859911
AllCCS[M+NH4]+217.832859911
AllCCS[M+Na]+218.232859911
AllCCS[M-H]-211.732859911
AllCCS[M+Na-2H]-213.832859911
AllCCS[M+HCOO]-216.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
HederageninCC1(C)CCC2(CCC3(C)C(=CCC4C5(C)CCC(O)C(C)(CO)C5CCC34C)C2C1)C(O)=O3025.0Standard polar33892256
HederageninCC1(C)CCC2(CCC3(C)C(=CCC4C5(C)CCC(O)C(C)(CO)C5CCC34C)C2C1)C(O)=O3631.4Standard non polar33892256
HederageninCC1(C)CCC2(CCC3(C)C(=CCC4C5(C)CCC(O)C(C)(CO)C5CCC34C)C2C1)C(O)=O4009.3Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Hederagenin GC-MS (Non-derivatized) - 70eV, Positivesplash10-0a4u-0023900000-5fd0673687f27073b3542021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Hederagenin GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Hederagenin GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Hederagenin GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Hederagenin GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Hederagenin GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Hederagenin GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Hederagenin GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Hederagenin GC-MS (TMS_3_1) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Hederagenin GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Hederagenin GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Hederagenin GC-MS (TBDMS_1_3) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Hederagenin GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Hederagenin GC-MS (TBDMS_2_2) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Hederagenin GC-MS (TBDMS_2_3) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Hederagenin GC-MS (TBDMS_3_1) - 70eV, PositiveNot Available2021-11-04Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hederagenin 10V, Positive-QTOFsplash10-0a4i-0000900000-7a532f41e2b0a36ceae42015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hederagenin 20V, Positive-QTOFsplash10-0a4r-0000900000-18713e516922a7682a2f2015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hederagenin 40V, Positive-QTOFsplash10-0a4i-3454900000-09817b569d56b06215042015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hederagenin 10V, Negative-QTOFsplash10-00di-0000900000-25d76a416e81894bdfa52015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hederagenin 20V, Negative-QTOFsplash10-0kos-0001900000-fb3ca1294d877cdf8c752015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hederagenin 40V, Negative-QTOFsplash10-0002-0005900000-71e61598cda51bbd128d2015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hederagenin 10V, Negative-QTOFsplash10-00di-0000900000-ce83f241675374237da42021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hederagenin 20V, Negative-QTOFsplash10-00di-0000900000-c6fd1f45c4dc2e908daa2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hederagenin 40V, Negative-QTOFsplash10-00di-0000900000-4e052cf43307f87dbb772021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hederagenin 10V, Positive-QTOFsplash10-05fr-0000900000-ef5f73120e1b51d1f5ed2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hederagenin 20V, Positive-QTOFsplash10-0a4i-0223900000-7e35d2ec875c5da32ebb2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hederagenin 40V, Positive-QTOFsplash10-00kr-0930000000-02fa19611c0e1539d40b2021-10-12Wishart 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 IDFDB030901
KNApSAcK IDC00003527
Chemspider ID226868
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkHederagenin
METLIN IDNot Available
PubChem Compound258538
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 ]