Hmdb loader

Showing metabocard for loganate (HMDB0304409)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 09:33:38 UTC
Update Date2021-09-24 09:33:38 UTC
HMDB IDHMDB0304409
Secondary Accession NumbersNone
Metabolite Identification
Common Nameloganate
DescriptionLoganate is also known as loganic acid. Loganate is soluble (in water) and a weakly acidic compound (based on its pKa). Loganate can be found in a number of food items such as hedge mustard, cinnamon, common sage, and welsh onion, which makes loganate a potential biomarker for the consumption of these food products. Loganic acid is an iridoid. Loganic acid is synthesized from 7-deoxyloganic acid by the enzyme 7-deoxyloganic acid hydroxylase (7-DLH). It is a substrate for the enzyme loganate O-methyltransferase for the production of loganin .
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304409 (loganate)


  Mrv1533004241519062D          

 26 28  0  0  0  0            999 V2000
   -0.3984    0.7541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -2.7604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -2.7604    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.3556    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.3646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    0.9521    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4990    1.3646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4990    2.1896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    2.6021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    2.1896    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    3.4271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4990    3.8396    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2135    2.6021    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2135    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    0.1271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4534   -0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  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  2  0  0  0  0
  5 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
  7 14  1  0  0  0  0
 14 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  1  0  0  0  0
 19 20  1  0  0  0  0
 15 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 18 23  1  0  0  0  0
 17 24  1  0  0  0  0
 16 25  1  0  0  0  0
  3 26  1  0  0  0  0
M  CHG  1  13  -1
M  END
Download

3D MOL for HMDB0304409 (loganate)

HMDB0304409
     RDKit          3D
loganate
 49 51  0  0  0  0  0  0  0  0999 V2000
   -1.6046    0.6244   -2.1349 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8183   -0.6201   -1.2869 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2041   -1.1395   -1.6396 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8841   -0.2987   -2.5005 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9723   -1.2639   -0.3504 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8899   -1.2761    0.6859 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2980   -0.8000    2.0081 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6599   -0.9844    2.4710 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0368   -0.5772    3.6203 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5941   -1.6171    1.6603 O   0  0  0  0  0  1  0  0  0  0  0  0
   -2.3899   -0.2035    2.7545 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0680   -0.0232    2.3088 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6907   -0.3414    0.9579 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3153    0.5029    0.5143 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4710   -0.1635    0.1502 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4582    0.2119    1.0573 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0229    1.4431    0.7394 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8734    1.8703    1.9173 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4863    3.0955    1.7020 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9750    1.2759   -0.4472 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2597    1.0270    0.0356 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4464    0.1102   -1.2502 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9305   -1.1135   -0.8078 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9193    0.0694   -1.2492 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5838   -0.9936   -2.1122 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9281   -0.2104    0.1340 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6046    1.1459   -2.1560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4071    0.3649   -3.2019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8488    1.2993   -1.7043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0447   -1.3752   -1.4175 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0442   -2.1428   -2.1170 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5574    0.2287   -1.9970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7214   -0.4887   -0.2038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4563   -2.2626   -0.3525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3580   -2.2246    0.7248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6757    0.1554    3.7370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3830   -1.4178    0.9364 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3017   -1.2467    0.3048 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2847    2.1892    0.4359 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2046    1.8883    2.7996 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6075    1.0520    2.1012 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4195    3.3630    0.7621 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9561    2.1668   -1.1018 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4385    0.0551    0.1288 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7325    0.2213   -2.3293 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5093   -1.5528   -1.4933 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5322    1.0132   -1.7018 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8244   -1.8173   -1.5981 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4128    0.7810    0.2331 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
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  7 11  2  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 17 20  1  0
 20 21  1  0
 20 22  1  0
 22 23  1  0
 22 24  1  0
 24 25  1  0
 13 26  1  0
 26  2  1  0
 26  6  1  0
 24 15  1  0
  1 27  1  0
  1 28  1  0
  1 29  1  0
  2 30  1  0
  3 31  1  0
  4 32  1  0
  5 33  1  0
  5 34  1  0
  6 35  1  0
 11 36  1  0
 13 37  1  0
 15 38  1  0
 17 39  1  0
 18 40  1  0
 18 41  1  0
 19 42  1  0
 20 43  1  0
 21 44  1  0
 22 45  1  0
 23 46  1  0
 24 47  1  0
 25 48  1  0
 26 49  1  0
M  CHG  1  10  -1
M  END
Download

3D SDF for HMDB0304409 (loganate)


  Mrv1533004241519062D          

 26 28  0  0  0  0            999 V2000
   -0.3984    0.7541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -2.7604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -2.7604    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.3556    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.3646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    0.9521    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4990    1.3646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4990    2.1896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    2.6021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    2.1896    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    3.4271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4990    3.8396    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2135    2.6021    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2135    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    0.1271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4534   -0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  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  2  0  0  0  0
  5 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
  7 14  1  0  0  0  0
 14 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  1  0  0  0  0
 19 20  1  0  0  0  0
 15 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 18 23  1  0  0  0  0
 17 24  1  0  0  0  0
 16 25  1  0  0  0  0
  3 26  1  0  0  0  0
M  CHG  1  13  -1
M  END
> <DATABASE_ID>
HMDB0304409

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1C(O)CC2C1C(OC1OC(CO)C(O)C(O)C1O)OC=C2C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C16H24O10/c1-5-8(18)2-6-7(14(22)23)4-24-15(10(5)6)26-16-13(21)12(20)11(19)9(3-17)25-16/h4-6,8-13,15-21H,2-3H2,1H3,(H,22,23)/p-1

> <INCHI_KEY>
JNNGEAWILNVFFD-UHFFFAOYSA-M

> <FORMULA>
C16H23O10

> <MOLECULAR_WEIGHT>
375.351

> <EXACT_MASS>
375.129670521

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
49

> <JCHEM_AVERAGE_POLARIZABILITY>
35.919924521038936

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-hydroxy-7-methyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylate

> <ALOGPS_LOGP>
-1.71

> <JCHEM_LOGP>
-2.216372853666667

> <ALOGPS_LOGS>
-0.83

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.206193523365306

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.257309327635798

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8340462513225235

> <JCHEM_POLAR_SURFACE_AREA>
168.97

> <JCHEM_REFRACTIVITY>
93.54239999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.77e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-hydroxy-7-methyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0304409 (loganate)

HMDB0304409
     RDKit          3D
loganate
 49 51  0  0  0  0  0  0  0  0999 V2000
   -1.6046    0.6244   -2.1349 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8183   -0.6201   -1.2869 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2041   -1.1395   -1.6396 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8841   -0.2987   -2.5005 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9723   -1.2639   -0.3504 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8899   -1.2761    0.6859 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2980   -0.8000    2.0081 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6599   -0.9844    2.4710 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0368   -0.5772    3.6203 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5941   -1.6171    1.6603 O   0  0  0  0  0  1  0  0  0  0  0  0
   -2.3899   -0.2035    2.7545 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0680   -0.0232    2.3088 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6907   -0.3414    0.9579 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3153    0.5029    0.5143 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4710   -0.1635    0.1502 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4582    0.2119    1.0573 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0229    1.4431    0.7394 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8734    1.8703    1.9173 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4863    3.0955    1.7020 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9750    1.2759   -0.4472 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2597    1.0270    0.0356 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4464    0.1102   -1.2502 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9305   -1.1135   -0.8078 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9193    0.0694   -1.2492 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5838   -0.9936   -2.1122 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9281   -0.2104    0.1340 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6046    1.1459   -2.1560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4071    0.3649   -3.2019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8488    1.2993   -1.7043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0447   -1.3752   -1.4175 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0442   -2.1428   -2.1170 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5574    0.2287   -1.9970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7214   -0.4887   -0.2038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4563   -2.2626   -0.3525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3580   -2.2246    0.7248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6757    0.1554    3.7370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3830   -1.4178    0.9364 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3017   -1.2467    0.3048 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2847    2.1892    0.4359 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2046    1.8883    2.7996 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6075    1.0520    2.1012 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4195    3.3630    0.7621 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9561    2.1668   -1.1018 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4385    0.0551    0.1288 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7325    0.2213   -2.3293 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5093   -1.5528   -1.4933 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5322    1.0132   -1.7018 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8244   -1.8173   -1.5981 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4128    0.7810    0.2331 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
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  7 11  2  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 17 20  1  0
 20 21  1  0
 20 22  1  0
 22 23  1  0
 22 24  1  0
 24 25  1  0
 13 26  1  0
 26  2  1  0
 26  6  1  0
 24 15  1  0
  1 27  1  0
  1 28  1  0
  1 29  1  0
  2 30  1  0
  3 31  1  0
  4 32  1  0
  5 33  1  0
  5 34  1  0
  6 35  1  0
 11 36  1  0
 13 37  1  0
 15 38  1  0
 17 39  1  0
 18 40  1  0
 18 41  1  0
 19 42  1  0
 20 43  1  0
 21 44  1  0
 22 45  1  0
 23 46  1  0
 24 47  1  0
 25 48  1  0
 26 49  1  0
M  CHG  1  10  -1
M  END
Download

PDB for HMDB0304409 (loganate)

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0      -0.744   1.408   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.268  -0.057   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.173  -1.303   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.268  -2.549   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.197  -2.073   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.197  -0.533   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.530   0.237   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       3.864  -0.533   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       3.864  -2.073   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.530  -2.843   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.530  -4.383   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       3.864  -5.153   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       1.197  -5.153   0.000  0.00  0.00           O-1
HETATM   14  O   UNK     0       2.530   1.777   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       3.864   2.547   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.198   1.777   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.531   2.547   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.531   4.087   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.198   4.857   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       3.864   4.087   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       5.198   6.397   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       6.531   7.167   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       7.865   4.857   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       7.865   1.777   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       5.198   0.237   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -2.713  -1.303   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4   26                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    2    7                                                  
CONECT    7    6    8   14                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    5   11                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14    7   15                                                       
CONECT   15   14   16   20                                                  
CONECT   16   15   17   25                                                  
CONECT   17   16   18   24                                                  
CONECT   18   17   19   23                                                  
CONECT   19   18   20   21                                                  
CONECT   20   19   15                                                       
CONECT   21   19   22                                                       
CONECT   22   21                                                            
CONECT   23   18                                                            
CONECT   24   17                                                            
CONECT   25   16                                                            
CONECT   26    3                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   56    0
END
Download

3D PDB for HMDB0304409 (loganate)

COMPND    HMDB0304409
HETATM    1  C1  UNL     1      -1.605   0.624  -2.135  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.818  -0.620  -1.287  1.00  0.00           C  
HETATM    3  C3  UNL     1      -3.204  -1.140  -1.640  1.00  0.00           C  
HETATM    4  O1  UNL     1      -3.884  -0.299  -2.500  1.00  0.00           O  
HETATM    5  C4  UNL     1      -3.972  -1.264  -0.350  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.890  -1.276   0.686  1.00  0.00           C  
HETATM    7  C6  UNL     1      -3.298  -0.800   2.008  1.00  0.00           C  
HETATM    8  C7  UNL     1      -4.660  -0.984   2.471  1.00  0.00           C  
HETATM    9  O2  UNL     1      -5.037  -0.577   3.620  1.00  0.00           O  
HETATM   10  O3  UNL     1      -5.594  -1.617   1.660  1.00  0.00           O1-
HETATM   11  C8  UNL     1      -2.390  -0.204   2.754  1.00  0.00           C  
HETATM   12  O4  UNL     1      -1.068  -0.023   2.309  1.00  0.00           O  
HETATM   13  C9  UNL     1      -0.691  -0.341   0.958  1.00  0.00           C  
HETATM   14  O5  UNL     1       0.315   0.503   0.514  1.00  0.00           O  
HETATM   15  C10 UNL     1       1.471  -0.164   0.150  1.00  0.00           C  
HETATM   16  O6  UNL     1       2.458   0.212   1.057  1.00  0.00           O  
HETATM   17  C11 UNL     1       3.023   1.443   0.739  1.00  0.00           C  
HETATM   18  C12 UNL     1       3.873   1.870   1.917  1.00  0.00           C  
HETATM   19  O7  UNL     1       4.486   3.095   1.702  1.00  0.00           O  
HETATM   20  C13 UNL     1       3.975   1.276  -0.447  1.00  0.00           C  
HETATM   21  O8  UNL     1       5.260   1.027   0.036  1.00  0.00           O  
HETATM   22  C14 UNL     1       3.446   0.110  -1.250  1.00  0.00           C  
HETATM   23  O9  UNL     1       3.930  -1.114  -0.808  1.00  0.00           O  
HETATM   24  C15 UNL     1       1.919   0.069  -1.249  1.00  0.00           C  
HETATM   25  O10 UNL     1       1.584  -0.994  -2.112  1.00  0.00           O  
HETATM   26  C16 UNL     1      -1.928  -0.210   0.134  1.00  0.00           C  
HETATM   27  H1  UNL     1      -2.605   1.146  -2.156  1.00  0.00           H  
HETATM   28  H2  UNL     1      -1.407   0.365  -3.202  1.00  0.00           H  
HETATM   29  H3  UNL     1      -0.849   1.299  -1.704  1.00  0.00           H  
HETATM   30  H4  UNL     1      -1.045  -1.375  -1.417  1.00  0.00           H  
HETATM   31  H5  UNL     1      -3.044  -2.143  -2.117  1.00  0.00           H  
HETATM   32  H6  UNL     1      -4.557   0.229  -1.997  1.00  0.00           H  
HETATM   33  H7  UNL     1      -4.721  -0.489  -0.204  1.00  0.00           H  
HETATM   34  H8  UNL     1      -4.456  -2.263  -0.352  1.00  0.00           H  
HETATM   35  H9  UNL     1      -2.358  -2.225   0.725  1.00  0.00           H  
HETATM   36  H10 UNL     1      -2.676   0.155   3.737  1.00  0.00           H  
HETATM   37  H11 UNL     1      -0.383  -1.418   0.936  1.00  0.00           H  
HETATM   38  H12 UNL     1       1.302  -1.247   0.305  1.00  0.00           H  
HETATM   39  H13 UNL     1       2.285   2.189   0.436  1.00  0.00           H  
HETATM   40  H14 UNL     1       3.205   1.888   2.800  1.00  0.00           H  
HETATM   41  H15 UNL     1       4.607   1.052   2.101  1.00  0.00           H  
HETATM   42  H16 UNL     1       4.419   3.363   0.762  1.00  0.00           H  
HETATM   43  H17 UNL     1       3.956   2.167  -1.102  1.00  0.00           H  
HETATM   44  H18 UNL     1       5.438   0.055   0.129  1.00  0.00           H  
HETATM   45  H19 UNL     1       3.732   0.221  -2.329  1.00  0.00           H  
HETATM   46  H20 UNL     1       4.509  -1.553  -1.493  1.00  0.00           H  
HETATM   47  H21 UNL     1       1.532   1.013  -1.702  1.00  0.00           H  
HETATM   48  H22 UNL     1       1.824  -1.817  -1.598  1.00  0.00           H  
HETATM   49  H23 UNL     1      -2.413   0.781   0.233  1.00  0.00           H  
CONECT    1    2   27   28   29
CONECT    2    3   26   30
CONECT    3    4    5   31
CONECT    4   32
CONECT    5    6   33   34
CONECT    6    7   26   35
CONECT    7    8   11   11
CONECT    8    9    9   10
CONECT   11   12   36
CONECT   12   13
CONECT   13   14   26   37
CONECT   14   15
CONECT   15   16   24   38
CONECT   16   17
CONECT   17   18   20   39
CONECT   18   19   40   41
CONECT   19   42
CONECT   20   21   22   43
CONECT   21   44
CONECT   22   23   24   45
CONECT   23   46
CONECT   24   25   47
CONECT   25   48
CONECT   26   49
END
Download

SMILES for HMDB0304409 (loganate)

CC1C(O)CC2C1C(OC1OC(CO)C(O)C(O)C1O)OC=C2C([O-])=O
Download

INCHI for HMDB0304409 (loganate)

InChI=1S/C16H24O10/c1-5-8(18)2-6-7(14(22)23)4-24-15(10(5)6)26-16-13(21)12(20)11(19)9(3-17)25-16/h4-6,8-13,15-21H,2-3H2,1H3,(H,22,23)/p-1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
6-Hydroxy-7-methyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1H,4ah,5H,6H,7H,7ah-cyclopenta[c]pyran-4-carboxylic acidGenerator
Loganic acidGenerator
Chemical FormulaC16H23O10
Average Molecular Weight375.351
Monoisotopic Molecular Weight375.129670521
IUPAC Name6-hydroxy-7-methyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylate
Traditional Name6-hydroxy-7-methyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-4-carboxylate
CAS Registry NumberNot Available
SMILES
CC1C(O)CC2C1C(OC1OC(CO)C(O)C(O)C1O)OC=C2C([O-])=O
InChI Identifier
InChI=1S/C16H24O10/c1-5-8(18)2-6-7(14(22)23)4-24-15(10(5)6)26-16-13(21)12(20)11(19)9(3-17)25-16/h4-6,8-13,15-21H,2-3H2,1H3,(H,22,23)/p-1
InChI KeyJNNGEAWILNVFFD-UHFFFAOYSA-M
Chemical Taxonomy
Description Belongs to the class of organic compounds known as iridoid o-glycosides. These are iridoid monoterpenes containing a glycosyl (usually a pyranosyl) moiety linked to the iridoid skeleton.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassTerpene glycosides
Direct ParentIridoid O-glycosides
Alternative Parents
Substituents
  • Iridoid o-glycoside
  • Hexose monosaccharide
  • Glycosyl compound
  • Iridoid-skeleton
  • O-glycosyl compound
  • Bicyclic monoterpenoid
  • Monoterpenoid
  • Monosaccharide
  • Oxane
  • Cyclic alcohol
  • Vinylogous ester
  • Secondary alcohol
  • Polyol
  • Carboxylic acid derivative
  • Carboxylic acid
  • Organoheterocyclic compound
  • Monocarboxylic acid or derivatives
  • Oxacycle
  • Acetal
  • Primary alcohol
  • Organooxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Alcohol
  • Carbonyl group
  • Organic oxygen compound
  • Organic anion
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
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
logP-1.7ALOGPS
logP-2.2ChemAxon
logS-0.83ALOGPS
pKa (Strongest Acidic)4.26ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area168.97 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity93.54 m³·mol⁻¹ChemAxon
Polarizability35.92 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+185.72832859911
AllCCS[M+H-H2O]+183.0432859911
AllCCS[M+Na]+188.91432859911
AllCCS[M+NH4]+188.20532859911
AllCCS[M-H]-183.66932859911
AllCCS[M+Na-2H]-183.22232859911
AllCCS[M+HCOO]-182.87232859911
DeepCCS[M+H]+180.69130932474
DeepCCS[M-H]-178.33330932474
DeepCCS[M-2H]-211.23230932474
DeepCCS[M+Na]+186.87430932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - loganate 10V, Negative-QTOFsplash10-0a4i-0379000000-dd6c296faf686956a5002019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - loganate 20V, Negative-QTOFsplash10-03dj-1916000000-c84975856bfbc7d0b9ad2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - loganate 40V, Negative-QTOFsplash10-0006-5900000000-9d96f2a1e072459a1a6a2019-02-23Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030983
KNApSAcK IDNot Available
Chemspider ID24785171
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
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 ReferencesNot Available