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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-09-24 07:21:17 UTC

Update Date

2021-09-24 07:21:17 UTC

HMDB ID

HMDB0304121

Secondary Accession Numbers

None

Metabolite Identification

Common Name

3-dehydrocholate

Description

3-dehydrocholate is practically insoluble (in water) and a weakly acidic compound (based on its pKa). 3-dehydrocholate can be found in a number of food items such as kale, cucurbita (gourd), atlantic herring, and spearmint, which makes 3-dehydrocholate a potential biomarker for the consumption of these food products. Dehydrocholic acid is a synthetic bile acid, manufactured by the oxidation of cholic acid. It acts as a hydrocholeretic, increasing bile output to clear increased bile acid load .

Structure

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


  Mrv1533005141521392D          

 29 32  0  0  0  0            999 V2000
    2.8728   -3.9050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5619   -3.1408    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7447   -3.0280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2383   -3.6793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4211   -3.5665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0853   -4.2178    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1102   -2.8023    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.0683   -2.4895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8390   -1.6970    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5218   -1.2340    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1731   -1.7404    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9853   -1.5952    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2655   -0.8192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7337   -0.1885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0777   -0.6740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6095   -1.3047    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4216   -1.1595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9534   -1.7902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7655   -1.6450    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6731   -2.5662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8610   -2.7114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3292   -2.0807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0489   -2.8566    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5171   -2.2259    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2368   -3.0018    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4247   -3.1470    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1444   -3.9229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8928   -2.5163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5330   -3.2587    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  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 16 22  1  0  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 28 29  1  0  0  0  0
  8 28  1  0  0  0  0
 11 28  1  0  0  0  0
 12 24  1  0  0  0  0
M  CHG  1   7  -1
M  END

HMDB0304121
     RDKit          3D
3-dehydrocholate
 66 69  0  0  0  0  0  0  0  0999 V2000
    3.5814   -0.5580   -1.6763 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5838    0.2239   -0.3944 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8847   -0.0282    0.3216 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1067    0.4009   -0.4731 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3325    0.1466    0.3079 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4467    0.6159    1.4581 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.3456   -0.6133   -0.2442 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.4095   -0.0488    0.4729 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2213   -1.4675    0.8565 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9329   -1.4235    1.6310 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3272   -0.0446    1.4040 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1313   -0.1792    1.2126 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9720    0.9616    1.6929 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7237    2.1945    1.1932 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4295    0.6405    1.6220 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7151   -0.6414    0.8757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2242   -0.6289    0.6181 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4446    0.6918   -0.0662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2373    1.4633    0.4560 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7036    0.9664   -1.2970 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2938    0.4865   -1.3445 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9611   -0.6492   -0.4625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4765   -1.9172   -1.1693 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5092   -0.8036   -0.0903 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5512   -0.5528   -1.2201 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3962    0.5838   -0.9977 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1136    0.7866   -2.1616 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1180    0.6021    0.2747 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3429    2.1008    0.6440 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5156   -1.2089   -1.6612 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7209    0.0878   -2.5585 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7269   -1.2654   -1.7904 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6542    1.3422   -0.6357 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0548   -1.1328    0.5101 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9097    0.4192    1.3553 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1678   -0.1525   -1.4222 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0266    1.4813   -0.7751 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7652    0.4090    1.4966 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1608   -2.1807    0.0098 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0544   -1.8546    1.4999 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1724   -1.5629    2.7043 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2276   -2.2290    1.3478 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5288    0.5670    2.3130 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3983   -0.9731    2.0090 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7481    1.0543    2.8081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4944    2.6862    0.8373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9739    1.4736    1.1313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9200    0.5257    2.6248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4332   -1.5470    1.4336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6886   -0.6259    1.6395 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5609   -1.4607   -0.0060 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3146    0.5868   -2.1513 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7409    2.0879   -1.4439 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1298    0.1267   -2.4081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6282    1.3648   -1.2402 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3920   -1.6388   -1.7282 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7452   -2.7041   -0.4568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7415   -2.3000   -1.8849 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4140   -1.9288    0.0723 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1417   -0.3394   -2.1300 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0782   -1.4289   -1.4946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2828    1.5073   -0.9899 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9474    0.1190   -2.8620 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8460    2.7564   -0.0975 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4185    2.3640    0.6103 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0022    2.2654    1.6854 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  1  0
  5  6  2  0
  5  7  1  0
  2  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  2  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
 25 26  1  0
 26 27  1  0
 26 28  1  0
 28 29  1  0
 28  8  1  0
 28 11  1  0
 24 12  1  0
 22 16  1  0
  1 30  1  0
  1 31  1  0
  1 32  1  0
  2 33  1  0
  3 34  1  0
  3 35  1  0
  4 36  1  0
  4 37  1  0
  8 38  1  0
  9 39  1  0
  9 40  1  0
 10 41  1  0
 10 42  1  0
 11 43  1  0
 12 44  1  0
 13 45  1  0
 14 46  1  0
 15 47  1  0
 15 48  1  0
 16 49  1  0
 17 50  1  0
 17 51  1  0
 20 52  1  0
 20 53  1  0
 21 54  1  0
 21 55  1  0
 23 56  1  0
 23 57  1  0
 23 58  1  0
 24 59  1  0
 25 60  1  0
 25 61  1  0
 26 62  1  0
 27 63  1  0
 29 64  1  0
 29 65  1  0
 29 66  1  0
M  CHG  1   7  -1
M  END


  Mrv1533005141521392D          

 29 32  0  0  0  0            999 V2000
    2.8728   -3.9050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5619   -3.1408    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7447   -3.0280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2383   -3.6793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4211   -3.5665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0853   -4.2178    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1102   -2.8023    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.0683   -2.4895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8390   -1.6970    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5218   -1.2340    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1731   -1.7404    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9853   -1.5952    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2655   -0.8192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7337   -0.1885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0777   -0.6740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6095   -1.3047    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4216   -1.1595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9534   -1.7902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7655   -1.6450    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6731   -2.5662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8610   -2.7114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3292   -2.0807    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0489   -2.8566    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5171   -2.2259    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2368   -3.0018    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4247   -3.1470    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1444   -3.9229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8928   -2.5163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5330   -3.2587    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  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 16 22  1  0  0  0  0
 22 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 28 29  1  0  0  0  0
  8 28  1  0  0  0  0
 11 28  1  0  0  0  0
 12 24  1  0  0  0  0
M  CHG  1   7  -1
M  END
> <DATABASE_ID>
HMDB0304121

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(CCC([O-])=O)C1CCC2C3C(O)CC4CC(=O)CCC4(C)C3CC(O)C12C

> <INCHI_IDENTIFIER>
InChI=1S/C24H38O5/c1-13(4-7-21(28)29)16-5-6-17-22-18(12-20(27)24(16,17)3)23(2)9-8-15(25)10-14(23)11-19(22)26/h13-14,16-20,22,26-27H,4-12H2,1-3H3,(H,28,29)/p-1

> <INCHI_KEY>
OEKUSRBIIZNLHZ-UHFFFAOYSA-M

> <FORMULA>
C24H37O5

> <MOLECULAR_WEIGHT>
405.556

> <EXACT_MASS>
405.264647871

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
45.96826130262153

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-{9,16-dihydroxy-2,15-dimethyl-5-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl}pentanoate

> <ALOGPS_LOGP>
2.75

> <JCHEM_LOGP>
2.6899952583333335

> <ALOGPS_LOGS>
-4.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
19.98667664437422

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.475012039836772

> <JCHEM_PKA_STRONGEST_BASIC>
-0.1783984748465538

> <JCHEM_POLAR_SURFACE_AREA>
97.66000000000001

> <JCHEM_REFRACTIVITY>
120.59829999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.81e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-{9,16-dihydroxy-2,15-dimethyl-5-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl}pentanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0304121
     RDKit          3D
3-dehydrocholate
 66 69  0  0  0  0  0  0  0  0999 V2000
    3.5814   -0.5580   -1.6763 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5838    0.2239   -0.3944 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8847   -0.0282    0.3216 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1067    0.4009   -0.4731 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3325    0.1466    0.3079 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4467    0.6159    1.4581 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.3456   -0.6133   -0.2442 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.4095   -0.0488    0.4729 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2213   -1.4675    0.8565 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9329   -1.4235    1.6310 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3272   -0.0446    1.4040 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1313   -0.1792    1.2126 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9720    0.9616    1.6929 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7237    2.1945    1.1932 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4295    0.6405    1.6220 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7151   -0.6414    0.8757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2242   -0.6289    0.6181 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4446    0.6918   -0.0662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2373    1.4633    0.4560 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7036    0.9664   -1.2970 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2938    0.4865   -1.3445 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9611   -0.6492   -0.4625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4765   -1.9172   -1.1693 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5092   -0.8036   -0.0903 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5512   -0.5528   -1.2201 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3962    0.5838   -0.9977 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1136    0.7866   -2.1616 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1180    0.6021    0.2747 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3429    2.1008    0.6440 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5156   -1.2089   -1.6612 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7209    0.0878   -2.5585 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7269   -1.2654   -1.7904 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6542    1.3422   -0.6357 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0548   -1.1328    0.5101 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9097    0.4192    1.3553 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1678   -0.1525   -1.4222 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0266    1.4813   -0.7751 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7652    0.4090    1.4966 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1608   -2.1807    0.0098 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0544   -1.8546    1.4999 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1724   -1.5629    2.7043 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2276   -2.2290    1.3478 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5288    0.5670    2.3130 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3983   -0.9731    2.0090 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7481    1.0543    2.8081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4944    2.6862    0.8373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9739    1.4736    1.1313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9200    0.5257    2.6248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4332   -1.5470    1.4336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6886   -0.6259    1.6395 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5609   -1.4607   -0.0060 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3146    0.5868   -2.1513 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7409    2.0879   -1.4439 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1298    0.1267   -2.4081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6282    1.3648   -1.2402 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3920   -1.6388   -1.7282 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7452   -2.7041   -0.4568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7415   -2.3000   -1.8849 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4140   -1.9288    0.0723 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1417   -0.3394   -2.1300 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0782   -1.4289   -1.4946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2828    1.5073   -0.9899 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9474    0.1190   -2.8620 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8460    2.7564   -0.0975 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4185    2.3640    0.6103 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0022    2.2654    1.6854 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  1  0
  5  6  2  0
  5  7  1  0
  2  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  2  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
 25 26  1  0
 26 27  1  0
 26 28  1  0
 28 29  1  0
 28  8  1  0
 28 11  1  0
 24 12  1  0
 22 16  1  0
  1 30  1  0
  1 31  1  0
  1 32  1  0
  2 33  1  0
  3 34  1  0
  3 35  1  0
  4 36  1  0
  4 37  1  0
  8 38  1  0
  9 39  1  0
  9 40  1  0
 10 41  1  0
 10 42  1  0
 11 43  1  0
 12 44  1  0
 13 45  1  0
 14 46  1  0
 15 47  1  0
 15 48  1  0
 16 49  1  0
 17 50  1  0
 17 51  1  0
 20 52  1  0
 20 53  1  0
 21 54  1  0
 21 55  1  0
 23 56  1  0
 23 57  1  0
 23 58  1  0
 24 59  1  0
 25 60  1  0
 25 61  1  0
 26 62  1  0
 27 63  1  0
 29 64  1  0
 29 65  1  0
 29 66  1  0
M  CHG  1   7  -1
M  END

HEADER    PROTEIN                                 14-MAY-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-15         0                                  
HETATM    1  C   UNK     0       5.363  -7.289   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.782  -5.863   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.257  -5.652   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.312  -6.868   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.786  -6.657   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.159  -7.873   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.206  -5.231   0.000  0.00  0.00           O-1
HETATM    8  C   UNK     0       5.727  -4.647   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.299  -3.168   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.574  -2.304   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.790  -3.249   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.306  -2.978   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.829  -1.529   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       8.836  -0.352   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      11.345  -1.258   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      12.338  -2.436   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      13.854  -2.164   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      14.846  -3.342   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      16.362  -3.071   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      14.323  -4.790   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      12.807  -5.061   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      11.814  -3.884   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      11.291  -5.332   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      10.299  -4.155   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       9.775  -5.603   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.259  -5.874   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       7.736  -7.323   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       7.267  -4.697   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.595  -6.083   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    2    9   28                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   28                                                  
CONECT   12   11   13   24                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17   22                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   16   24                                             
CONECT   23   22                                                            
CONECT   24   22   25   12                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29    8   11                                             
CONECT   29   28                                                            
MASTER        0    0    0    0    0    0    0    0   29    0   64    0
END

COMPND    HMDB0304121
HETATM    1  C1  UNL     1       3.581  -0.558  -1.676  1.00  0.00           C  
HETATM    2  C2  UNL     1       3.584   0.224  -0.394  1.00  0.00           C  
HETATM    3  C3  UNL     1       4.885  -0.028   0.322  1.00  0.00           C  
HETATM    4  C4  UNL     1       6.107   0.401  -0.473  1.00  0.00           C  
HETATM    5  C5  UNL     1       7.332   0.147   0.308  1.00  0.00           C  
HETATM    6  O1  UNL     1       7.447   0.616   1.458  1.00  0.00           O  
HETATM    7  O2  UNL     1       8.346  -0.613  -0.244  1.00  0.00           O1-
HETATM    8  C6  UNL     1       2.410  -0.049   0.473  1.00  0.00           C  
HETATM    9  C7  UNL     1       2.221  -1.468   0.857  1.00  0.00           C  
HETATM   10  C8  UNL     1       0.933  -1.424   1.631  1.00  0.00           C  
HETATM   11  C9  UNL     1       0.327  -0.045   1.404  1.00  0.00           C  
HETATM   12  C10 UNL     1      -1.131  -0.179   1.213  1.00  0.00           C  
HETATM   13  C11 UNL     1      -1.972   0.962   1.693  1.00  0.00           C  
HETATM   14  O3  UNL     1      -1.724   2.195   1.193  1.00  0.00           O  
HETATM   15  C12 UNL     1      -3.430   0.640   1.622  1.00  0.00           C  
HETATM   16  C13 UNL     1      -3.715  -0.641   0.876  1.00  0.00           C  
HETATM   17  C14 UNL     1      -5.224  -0.629   0.618  1.00  0.00           C  
HETATM   18  C15 UNL     1      -5.445   0.692  -0.066  1.00  0.00           C  
HETATM   19  O4  UNL     1      -6.237   1.463   0.456  1.00  0.00           O  
HETATM   20  C16 UNL     1      -4.704   0.966  -1.297  1.00  0.00           C  
HETATM   21  C17 UNL     1      -3.294   0.486  -1.345  1.00  0.00           C  
HETATM   22  C18 UNL     1      -2.961  -0.649  -0.462  1.00  0.00           C  
HETATM   23  C19 UNL     1      -3.477  -1.917  -1.169  1.00  0.00           C  
HETATM   24  C20 UNL     1      -1.509  -0.804  -0.090  1.00  0.00           C  
HETATM   25  C21 UNL     1      -0.551  -0.553  -1.220  1.00  0.00           C  
HETATM   26  C22 UNL     1       0.396   0.584  -0.998  1.00  0.00           C  
HETATM   27  O5  UNL     1       1.114   0.787  -2.162  1.00  0.00           O  
HETATM   28  C23 UNL     1       1.118   0.602   0.275  1.00  0.00           C  
HETATM   29  C24 UNL     1       1.343   2.101   0.644  1.00  0.00           C  
HETATM   30  H1  UNL     1       4.516  -1.209  -1.661  1.00  0.00           H  
HETATM   31  H2  UNL     1       3.721   0.088  -2.559  1.00  0.00           H  
HETATM   32  H3  UNL     1       2.727  -1.265  -1.790  1.00  0.00           H  
HETATM   33  H4  UNL     1       3.654   1.342  -0.636  1.00  0.00           H  
HETATM   34  H5  UNL     1       5.055  -1.133   0.510  1.00  0.00           H  
HETATM   35  H6  UNL     1       4.910   0.419   1.355  1.00  0.00           H  
HETATM   36  H7  UNL     1       6.168  -0.152  -1.422  1.00  0.00           H  
HETATM   37  H8  UNL     1       6.027   1.481  -0.775  1.00  0.00           H  
HETATM   38  H9  UNL     1       2.765   0.409   1.497  1.00  0.00           H  
HETATM   39  H10 UNL     1       2.161  -2.181   0.010  1.00  0.00           H  
HETATM   40  H11 UNL     1       3.054  -1.855   1.500  1.00  0.00           H  
HETATM   41  H12 UNL     1       1.172  -1.563   2.704  1.00  0.00           H  
HETATM   42  H13 UNL     1       0.228  -2.229   1.348  1.00  0.00           H  
HETATM   43  H14 UNL     1       0.529   0.567   2.313  1.00  0.00           H  
HETATM   44  H15 UNL     1      -1.398  -0.973   2.009  1.00  0.00           H  
HETATM   45  H16 UNL     1      -1.748   1.054   2.808  1.00  0.00           H  
HETATM   46  H17 UNL     1      -2.494   2.686   0.837  1.00  0.00           H  
HETATM   47  H18 UNL     1      -3.974   1.474   1.131  1.00  0.00           H  
HETATM   48  H19 UNL     1      -3.920   0.526   2.625  1.00  0.00           H  
HETATM   49  H20 UNL     1      -3.433  -1.547   1.434  1.00  0.00           H  
HETATM   50  H21 UNL     1      -5.689  -0.626   1.640  1.00  0.00           H  
HETATM   51  H22 UNL     1      -5.561  -1.461  -0.006  1.00  0.00           H  
HETATM   52  H23 UNL     1      -5.315   0.587  -2.151  1.00  0.00           H  
HETATM   53  H24 UNL     1      -4.741   2.088  -1.444  1.00  0.00           H  
HETATM   54  H25 UNL     1      -3.130   0.127  -2.408  1.00  0.00           H  
HETATM   55  H26 UNL     1      -2.628   1.365  -1.240  1.00  0.00           H  
HETATM   56  H27 UNL     1      -4.392  -1.639  -1.728  1.00  0.00           H  
HETATM   57  H28 UNL     1      -3.745  -2.704  -0.457  1.00  0.00           H  
HETATM   58  H29 UNL     1      -2.742  -2.300  -1.885  1.00  0.00           H  
HETATM   59  H30 UNL     1      -1.414  -1.929   0.072  1.00  0.00           H  
HETATM   60  H31 UNL     1      -1.142  -0.339  -2.130  1.00  0.00           H  
HETATM   61  H32 UNL     1       0.078  -1.429  -1.495  1.00  0.00           H  
HETATM   62  H33 UNL     1      -0.283   1.507  -0.990  1.00  0.00           H  
HETATM   63  H34 UNL     1       0.947   0.119  -2.862  1.00  0.00           H  
HETATM   64  H35 UNL     1       0.846   2.756  -0.097  1.00  0.00           H  
HETATM   65  H36 UNL     1       2.419   2.364   0.610  1.00  0.00           H  
HETATM   66  H37 UNL     1       1.002   2.265   1.685  1.00  0.00           H  
CONECT    1    2   30   31   32
CONECT    2    3    8   33
CONECT    3    4   34   35
CONECT    4    5   36   37
CONECT    5    6    6    7
CONECT    8    9   28   38
CONECT    9   10   39   40
CONECT   10   11   41   42
CONECT   11   12   28   43
CONECT   12   13   24   44
CONECT   13   14   15   45
CONECT   14   46
CONECT   15   16   47   48
CONECT   16   17   22   49
CONECT   17   18   50   51
CONECT   18   19   19   20
CONECT   20   21   52   53
CONECT   21   22   54   55
CONECT   22   23   24
CONECT   23   56   57   58
CONECT   24   25   59
CONECT   25   26   60   61
CONECT   26   27   28   62
CONECT   27   63
CONECT   28   29
CONECT   29   64   65   66
END

HMDB0304121
     RDKit          3D
3-dehydrocholate
 66 69  0  0  0  0  0  0  0  0999 V2000
    3.5814   -0.5580   -1.6763 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5838    0.2239   -0.3944 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8847   -0.0282    0.3216 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1067    0.4009   -0.4731 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3325    0.1466    0.3079 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4467    0.6159    1.4581 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.3456   -0.6133   -0.2442 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.4095   -0.0488    0.4729 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2213   -1.4675    0.8565 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9329   -1.4235    1.6310 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3272   -0.0446    1.4040 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1313   -0.1792    1.2126 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9720    0.9616    1.6929 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7237    2.1945    1.1932 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4295    0.6405    1.6220 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7151   -0.6414    0.8757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2242   -0.6289    0.6181 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4446    0.6918   -0.0662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2373    1.4633    0.4560 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7036    0.9664   -1.2970 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2938    0.4865   -1.3445 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9611   -0.6492   -0.4625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4765   -1.9172   -1.1693 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5092   -0.8036   -0.0903 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5512   -0.5528   -1.2201 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3962    0.5838   -0.9977 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1136    0.7866   -2.1616 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1180    0.6021    0.2747 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3429    2.1008    0.6440 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5156   -1.2089   -1.6612 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7209    0.0878   -2.5585 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7269   -1.2654   -1.7904 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6542    1.3422   -0.6357 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0548   -1.1328    0.5101 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9097    0.4192    1.3553 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1678   -0.1525   -1.4222 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0266    1.4813   -0.7751 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7652    0.4090    1.4966 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1608   -2.1807    0.0098 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0544   -1.8546    1.4999 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1724   -1.5629    2.7043 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2276   -2.2290    1.3478 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5288    0.5670    2.3130 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3983   -0.9731    2.0090 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7481    1.0543    2.8081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4944    2.6862    0.8373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9739    1.4736    1.1313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9200    0.5257    2.6248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4332   -1.5470    1.4336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6886   -0.6259    1.6395 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5609   -1.4607   -0.0060 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3146    0.5868   -2.1513 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7409    2.0879   -1.4439 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1298    0.1267   -2.4081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6282    1.3648   -1.2402 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3920   -1.6388   -1.7282 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7452   -2.7041   -0.4568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7415   -2.3000   -1.8849 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4140   -1.9288    0.0723 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1417   -0.3394   -2.1300 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0782   -1.4289   -1.4946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2828    1.5073   -0.9899 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9474    0.1190   -2.8620 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8460    2.7564   -0.0975 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4185    2.3640    0.6103 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0022    2.2654    1.6854 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  1  0
  5  6  2  0
  5  7  1  0
  2  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  2  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
 25 26  1  0
 26 27  1  0
 26 28  1  0
 28 29  1  0
 28  8  1  0
 28 11  1  0
 24 12  1  0
 22 16  1  0
  1 30  1  0
  1 31  1  0
  1 32  1  0
  2 33  1  0
  3 34  1  0
  3 35  1  0
  4 36  1  0
  4 37  1  0
  8 38  1  0
  9 39  1  0
  9 40  1  0
 10 41  1  0
 10 42  1  0
 11 43  1  0
 12 44  1  0
 13 45  1  0
 14 46  1  0
 15 47  1  0
 15 48  1  0
 16 49  1  0
 17 50  1  0
 17 51  1  0
 20 52  1  0
 20 53  1  0
 21 54  1  0
 21 55  1  0
 23 56  1  0
 23 57  1  0
 23 58  1  0
 24 59  1  0
 25 60  1  0
 25 61  1  0
 26 62  1  0
 27 63  1  0
 29 64  1  0
 29 65  1  0
 29 66  1  0
M  CHG  1   7  -1
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
3-Dehydrocholic acid	Generator

Chemical Formula

C₂₄H₃₇O₅

Average Molecular Weight

405.556

Monoisotopic Molecular Weight

405.264647871

IUPAC Name

4-{9,16-dihydroxy-2,15-dimethyl-5-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl}pentanoate

Traditional Name

4-{9,16-dihydroxy-2,15-dimethyl-5-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl}pentanoate

CAS Registry Number

Not Available

SMILES

CC(CCC([O-])=O)C1CCC2C3C(O)CC4CC(=O)CCC4(C)C3CC(O)C12C

InChI Identifier

InChI=1S/C24H38O5/c1-13(4-7-21(28)29)16-5-6-17-22-18(12-20(27)24(16,17)3)23(2)9-8-15(25)10-14(23)11-19(22)26/h13-14,16-20,22,26-27H,4-12H2,1-3H3,(H,28,29)/p-1

InChI Key

OEKUSRBIIZNLHZ-UHFFFAOYSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dihydroxy bile acids, alcohols and derivatives. Dihydroxy bile acids, alcohols and derivatives are compounds containing or derived from a bile acid or alcohol, and which bears exactly two carboxylic acid groups.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Bile acids, alcohols and derivatives

Direct Parent

Dihydroxy bile acids, alcohols and derivatives

Alternative Parents

Substituents

Dihydroxy bile acid, alcohol, or derivatives
3-oxosteroid
12-hydroxysteroid
Hydroxysteroid
7-hydroxysteroid
Oxosteroid
Cyclic alcohol
Cyclic ketone
Ketone
Secondary alcohol
Carboxylic acid
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Alcohol
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organooxygen compound
Organic anion
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

a bile acid (CPD-12452 )

Ontology

Not Available

Exogenous (HMDB: HMDB0304121)

Herbs and Spices (FooDB: FOOD00866)

Nut

Almond (FooDB: FOOD00148)
Brazil nut (FooDB: FOOD00024)
Cashew nut (FooDB: FOOD00011)
Chestnut (FooDB: FOOD00045)
Hazelnut (FooDB: FOOD00376)
Peanut (FooDB: FOOD00016)
Pecan nut (FooDB: FOOD00044)
Pine nut (FooDB: FOOD00138)
Pistachio (FooDB: FOOD00140)
Walnut (FooDB: FOOD00608)
Acorn (FooDB: FOOD00282)
Beech nut (FooDB: FOOD00299)
Butternut (FooDB: FOOD00316)
Chinese chestnut (FooDB: FOOD00331)
European chestnut (FooDB: FOOD00363)
Hickory nut (FooDB: FOOD00377)
Macadamia nut (FooDB: FOOD00525)
Mixed nuts (FooDB: FOOD00771)
Pili nut (FooDB: FOOD00432)
Colorado pinyon (FooDB: FOOD00433)
Black walnut (FooDB: FOOD00093)
Common walnut (FooDB: FOOD00094)
Japanese chestnut (FooDB: FOOD00385)
Common hazelnut (FooDB: FOOD00062)
Macadamia nut (M. tetraphylla) (FooDB: FOOD00225)
Japanese walnut (FooDB: FOOD00240)
Nuts (FooDB: FOOD00869)

Fruit

Pome

Drupe

Apricot (FooDB: FOOD00144)
Prunus (Cherry, Plum) (FooDB: FOOD00143)
Nectarine (FooDB: FOOD00229)
Peach (FooDB: FOOD00149)
European plum (FooDB: FOOD00147)
Sour cherry (FooDB: FOOD00146)
Sweet cherry (FooDB: FOOD00145)
Common chokecherry (FooDB: FOOD00562)
Peach (var.) (FooDB: FOOD00230)

Tropical fruit

Berry

Bilberry (FooDB: FOOD00193)
Rubus (Blackberry, Raspberry) (FooDB: FOOD00160)
Vaccinium (Blueberry, Cranberry, Huckleberry) (FooDB: FOOD00188)
Blackcurrant (FooDB: FOOD00155)
Redcurrant (FooDB: FOOD00156)
Elderberry (FooDB: FOOD00358)
Gooseberry (FooDB: FOOD00157)
Grape (FooDB: FOOD00369)
Lingonberry (FooDB: FOOD00194)
Loganberry (FooDB: FOOD00400)
Strawberry (FooDB: FOOD00083)
Boysenberry (FooDB: FOOD00542)
American cranberry (FooDB: FOOD00192)
Common grape (FooDB: FOOD00204)
Strawberry guava (FooDB: FOOD00482)
Black mulberry (FooDB: FOOD00117)
Red raspberry (FooDB: FOOD00162)
Muscadine grape (FooDB: FOOD00203)
Salmonberry (FooDB: FOOD00456)
Alaska blueberry (FooDB: FOOD00380)
Sea-buckthornberry (FooDB: FOOD00087)
Black elderberry (FooDB: FOOD00166)
Black crowberry (FooDB: FOOD00075)
Black huckleberry (FooDB: FOOD00084)
Mulberry (FooDB: FOOD00116)
Black chokeberry (FooDB: FOOD00136)
Cloudberry (FooDB: FOOD00161)
Black raspberry (FooDB: FOOD00163)
Rowanberry (FooDB: FOOD00176)
Lowbush blueberry (FooDB: FOOD00189)
Sparkleberry (FooDB: FOOD00190)
Highbush blueberry (FooDB: FOOD00191)
Arctic blackberry (FooDB: FOOD00207)
Bayberry (FooDB: FOOD00209)
Elliott's blueberry (FooDB: FOOD00210)
Canada blueberry (FooDB: FOOD00211)
Bog bilberry (FooDB: FOOD00212)
Buffalo currant (FooDB: FOOD00213)
European cranberry (FooDB: FOOD00217)
Deerberry (FooDB: FOOD00218)
Cascade huckleberry (FooDB: FOOD00220)
Oval-leaf huckleberry (FooDB: FOOD00221)
Evergreen huckleberry (FooDB: FOOD00222)
Red huckleberry (FooDB: FOOD00223)
Summer grape (FooDB: FOOD00227)
Fox grape (FooDB: FOOD00228)
Half-highbush blueberry (FooDB: FOOD00248)
Jostaberry (FooDB: FOOD00257)
Sweet rowanberry (FooDB: FOOD00265)
Skunk currant (FooDB: FOOD00267)
Squashberry (FooDB: FOOD00344)
Ohelo berry (FooDB: FOOD00419)
Chinese bayberry (FooDB: FOOD00852)
Saskatoon berry (FooDB: FOOD00884)
Nanking cherry (FooDB: FOOD00885)

Other fruit

Date (FooDB: FOOD00135)
Fig (FooDB: FOOD00081)
Jujube (FooDB: FOOD00388)

Citrus

Grapefruit (FooDB: FOOD00256)
Lemon (FooDB: FOOD00054)
Lime (FooDB: FOOD00053)
Sweet orange (FooDB: FOOD00057)
Mandarin orange (Clementine, Tangerine) (FooDB: FOOD00056)
Persian lime (FooDB: FOOD00543)
Pummelo (FooDB: FOOD00055)
Grapefruit/Pummelo hybrid (FooDB: FOOD00255)
Citrus (FooDB: FOOD00859)

Fruits (FooDB: FOOD00871)

Vegetable

Shoot vegetable

Fruit vegetable

Eggplant (FooDB: FOOD00174)
Avocado (FooDB: FOOD00130)
Groundcherry (FooDB: FOOD00371)
Olive (FooDB: FOOD00121)
Pepper (FooDB: FOOD00040)
Garden tomato (FooDB: FOOD00171)
Mexican groundcherry (FooDB: FOOD00491)
Green bell pepper (FooDB: FOOD00877)
Yellow bell pepper (FooDB: FOOD00878)
Red bell pepper (FooDB: FOOD00880)
Italian sweet red pepper (FooDB: FOOD00881)
Garden tomato (var.) (FooDB: FOOD00173)
Cherry tomato (FooDB: FOOD00172)
Pepper (C. baccatum) (FooDB: FOOD00231)
Pepper (C. chinense) (FooDB: FOOD00232)
Pepper (Capsicum) (FooDB: FOOD00233)
Pepper (C. frutescens) (FooDB: FOOD00428)
Pepper (C. pubescens) (FooDB: FOOD00849)
Orange bell pepper (FooDB: FOOD00879)

Root vegetable

Cabbage

Leaf vegetable

Lettuce (FooDB: FOOD00095)
Swiss chard (FooDB: FOOD00237)
Garden cress (FooDB: FOOD00099)
Endive (FooDB: FOOD00048)
Spinach (FooDB: FOOD00178)
Common beet (FooDB: FOOD00025)
Garland chrysanthemum (FooDB: FOOD00333)
Jute (FooDB: FOOD00389)
Lambsquarters (FooDB: FOOD00394)
New Zealand spinach (FooDB: FOOD00415)
Swamp cabbage (FooDB: FOOD00091)
Rocket salad (ssp.) (FooDB: FOOD00077)
Yautia (FooDB: FOOD00510)
Romaine lettuce (FooDB: FOOD00888)
Rocket salad (FooDB: FOOD00244)
Chicory leaves (FooDB: FOOD00250)
Corn salad (FooDB: FOOD00340)
Malabar spinach (FooDB: FOOD00404)
Ostrich fern (FooDB: FOOD00556)
Green vegetables (FooDB: FOOD00872)

Mushroom

Tuber

Onion-family vegetable

Leek (FooDB: FOOD00007)
Allium (FooDB: FOOD00005)
Wild leek (FooDB: FOOD00396)
Shallot (FooDB: FOOD00243)
Garden onion (FooDB: FOOD00006)
Garden onion (var.) (FooDB: FOOD00226)
Onion-family vegetables (FooDB: FOOD00855)
Green onion (FooDB: FOOD00963)
Red onion (FooDB: FOOD00962)

Other vegetable

Okra (FooDB: FOOD00420)
Horseradish tree (FooDB: FOOD00379)
Sacred lotus (FooDB: FOOD00402)
Tree fern (FooDB: FOOD00797)
Chinese water chestnut (FooDB: FOOD00332)
Nopal (FooDB: FOOD00416)
Carob (FooDB: FOOD00321)
Agave (FooDB: FOOD00563)
Narrowleaf cattail (FooDB: FOOD00564)
Giant butterbur (FooDB: FOOD00314)
Sesbania flower (FooDB: FOOD00469)

Stalk vegetable

Brassica

Brassicas (FooDB: FOOD00857)

Soy

Soy bean (FooDB: FOOD00085)

Soy product

Other soy product (FooDB: FOOD00271)

Cereal and cereal product

Other bread

Other bread (FooDB: FOOD00269)

Cereal

Cereal product

Dough

Sourdough (FooDB: FOOD00275)

Cereals and cereal products (FooDB: FOOD00858)

Pulse

Bean

Lentil

Lentils (FooDB: FOOD00098)

Pea

Other pulse

White lupine (FooDB: FOOD00403)
Lupine (FooDB: FOOD00104)

Pulses (FooDB: FOOD00867)

Abalone (FooDB: FOOD00279)
Conch (FooDB: FOOD00611)

Gourd

Chayote (FooDB: FOOD00325)
Cucumber (FooDB: FOOD00065)
Muskmelon (FooDB: FOOD00064)
Cucurbita (FooDB: FOOD00066)
Watermelon (FooDB: FOOD00052)
Bitter gourd (FooDB: FOOD00115)
Calabash (FooDB: FOOD00318)
Towel gourd (FooDB: FOOD00492)
Winter squash (FooDB: FOOD00283)
Butternut squash (FooDB: FOOD00317)
Wax gourd (FooDB: FOOD00499)
Green zucchini (FooDB: FOOD00875)
Yellow zucchini (FooDB: FOOD00876)
Japanese pumpkin (FooDB: FOOD00886)
Sunburst squash (pattypan squash) (FooDB: FOOD00874)
Tinda (FooDB: FOOD00559)
Horned melon (FooDB: FOOD00761)

Tea

Herbal tea

Greenthread tea (FooDB: FOOD00820)

Cocoa and cocoa product

Cocoa

Cocoa bean (FooDB: FOOD00182)

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	2.75	ALOGPS
logP	2.69	ChemAxon
logS	-4.4	ALOGPS
pKa (Strongest Acidic)	4.48	ChemAxon
pKa (Strongest Basic)	-0.18	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	97.66 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	120.6 m³·mol⁻¹	ChemAxon
Polarizability	45.97 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
AllCCS	[M+H]+	202.154	32859911
AllCCS	[M+H-H2O]+	199.959	32859911
AllCCS	[M+Na]+	204.747	32859911
AllCCS	[M+NH4]+	204.171	32859911
AllCCS	[M-H]-	200.582	32859911
AllCCS	[M+Na-2H]-	201.773	32859911
AllCCS	[M+HCOO]-	203.238	32859911
DeepCCS	[M-2H]-	231.58	30932474
DeepCCS	[M+Na]+	206.807	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	14.1171 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.1 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2893.8 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	214.7 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	208.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	172.7 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	432.7 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	611.8 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	629.6 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	88.0 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1078.9 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	530.9 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1583.0 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	341.6 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	445.0 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	241.4 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	268.2 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	64.5 seconds	40023050

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3-dehydrocholate,3TMS,isomer #1	CC(CCC(=O)[O-])C1CCC2C3C(O[Si](C)(C)C)CC4CC(O[Si](C)(C)C)=CCC4(C)C3CC(O[Si](C)(C)C)C12C	3402.0	Semi standard non polar	33892256
3-dehydrocholate,3TMS,isomer #1	CC(CCC(=O)[O-])C1CCC2C3C(O[Si](C)(C)C)CC4CC(O[Si](C)(C)C)=CCC4(C)C3CC(O[Si](C)(C)C)C12C	3220.6	Standard non polar	33892256
3-dehydrocholate,3TMS,isomer #1	CC(CCC(=O)[O-])C1CCC2C3C(O[Si](C)(C)C)CC4CC(O[Si](C)(C)C)=CCC4(C)C3CC(O[Si](C)(C)C)C12C	3523.5	Standard polar	33892256
3-dehydrocholate,3TMS,isomer #2	CC(CCC(=O)[O-])C1CCC2C3C(O[Si](C)(C)C)CC4C=C(O[Si](C)(C)C)CCC4(C)C3CC(O[Si](C)(C)C)C12C	3413.1	Semi standard non polar	33892256
3-dehydrocholate,3TMS,isomer #2	CC(CCC(=O)[O-])C1CCC2C3C(O[Si](C)(C)C)CC4C=C(O[Si](C)(C)C)CCC4(C)C3CC(O[Si](C)(C)C)C12C	3239.2	Standard non polar	33892256
3-dehydrocholate,3TMS,isomer #2	CC(CCC(=O)[O-])C1CCC2C3C(O[Si](C)(C)C)CC4C=C(O[Si](C)(C)C)CCC4(C)C3CC(O[Si](C)(C)C)C12C	3528.4	Standard polar	33892256
3-dehydrocholate,3TBDMS,isomer #1	CC(CCC(=O)[O-])C1CCC2C3C(O[Si](C)(C)C(C)(C)C)CC4CC(O[Si](C)(C)C(C)(C)C)=CCC4(C)C3CC(O[Si](C)(C)C(C)(C)C)C12C	4094.0	Semi standard non polar	33892256
3-dehydrocholate,3TBDMS,isomer #1	CC(CCC(=O)[O-])C1CCC2C3C(O[Si](C)(C)C(C)(C)C)CC4CC(O[Si](C)(C)C(C)(C)C)=CCC4(C)C3CC(O[Si](C)(C)C(C)(C)C)C12C	3763.1	Standard non polar	33892256
3-dehydrocholate,3TBDMS,isomer #1	CC(CCC(=O)[O-])C1CCC2C3C(O[Si](C)(C)C(C)(C)C)CC4CC(O[Si](C)(C)C(C)(C)C)=CCC4(C)C3CC(O[Si](C)(C)C(C)(C)C)C12C	3738.6	Standard polar	33892256
3-dehydrocholate,3TBDMS,isomer #2	CC(CCC(=O)[O-])C1CCC2C3C(O[Si](C)(C)C(C)(C)C)CC4C=C(O[Si](C)(C)C(C)(C)C)CCC4(C)C3CC(O[Si](C)(C)C(C)(C)C)C12C	4106.8	Semi standard non polar	33892256
3-dehydrocholate,3TBDMS,isomer #2	CC(CCC(=O)[O-])C1CCC2C3C(O[Si](C)(C)C(C)(C)C)CC4C=C(O[Si](C)(C)C(C)(C)C)CCC4(C)C3CC(O[Si](C)(C)C(C)(C)C)C12C	3866.9	Standard non polar	33892256
3-dehydrocholate,3TBDMS,isomer #2	CC(CCC(=O)[O-])C1CCC2C3C(O[Si](C)(C)C(C)(C)C)CC4C=C(O[Si](C)(C)C(C)(C)C)CCC4(C)C3CC(O[Si](C)(C)C(C)(C)C)C12C	3745.9	Standard polar	33892256

Spectra

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-dehydrocholate 10V, Negative-QTOF	splash10-000i-0009000000-5b16d66c4c8164f36725	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-dehydrocholate 20V, Negative-QTOF	splash10-000i-0009000000-a0052dfdc6d30c563128	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-dehydrocholate 40V, Negative-QTOF	splash10-052p-1009000000-8e85ac909603d99096bb	2019-02-23	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB030415

KNApSAcK ID

Not Available

Chemspider ID

21233824

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Dehydrocholic acid

METLIN ID

Not Available

PubChem Compound

73721376

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for 3-dehydrocholate (HMDB0304121)

MOL for HMDB0304121 (3-dehydrocholate)

3D MOL for HMDB0304121 (3-dehydrocholate)

3D SDF for HMDB0304121 (3-dehydrocholate)

3D-SDF for HMDB0304121 (3-dehydrocholate)

PDB for HMDB0304121 (3-dehydrocholate)

3D PDB for HMDB0304121 (3-dehydrocholate)

SMILES for HMDB0304121 (3-dehydrocholate)

INCHI for HMDB0304121 (3-dehydrocholate)

Structure for HMDB0304121 (3-dehydrocholate)

3D Structure for HMDB0304121 (3-dehydrocholate)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Derivatized

MS/MS Spectra