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Showing metabocard for 5-(3',4',5'-Trihydroxyphenyl)-gamma-valerolactone-4'-O-glucuronide (HMDB0059986)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2013-04-09 21:17:55 UTC
Update Date2021-09-14 15:39:02 UTC
HMDB IDHMDB0059986
Secondary Accession Numbers
  • HMDB59986
Metabolite Identification
Common Name5-(3',4',5'-Trihydroxyphenyl)-gamma-valerolactone-4'-O-glucuronide
Description5-(3',4',5'-Trihydroxyphenyl)-gamma-valerolactone-4'-O-glucuronide belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose. 5-(3',4',5'-Trihydroxyphenyl)-gamma-valerolactone-4'-O-glucuronide is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0059986 (5-(3',4',5'-Trihydroxyphenyl)-gamma-valerolactone-4'-O-glucuronide)

  Mrv1652303102016572D          

 34 36  0  0  1  0            999 V2000
    2.9049    5.4562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1599    4.6715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    6.7661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    8.0036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    6.7661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    7.1786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    5.9411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    8.4161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    7.1786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9849    4.6715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   10.4786    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.4302   10.8911    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.1447    9.6536    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.7158    8.0036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   10.4786    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0013   10.8911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    9.2411    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.0013    9.2411    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    6.7661    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4698    4.0041    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   10.8911    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   11.7161    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592    9.2411    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   10.4786    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   11.7161    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2398    5.4562    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    8.4161    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    9.6536    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3074    6.3156    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   11.3036    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   11.3036    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    8.8286    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   10.0661    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    8.8286    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  6  3  1  0  0  0  0
  6  4  2  0  0  0  0
  6  5  1  0  0  0  0
  7  1  1  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
  9  5  2  0  0  0  0
 10  2  1  0  0  0  0
 12 11  1  0  0  0  0
 13 11  1  0  0  0  0
 14  8  2  0  0  0  0
 14  9  1  0  0  0  0
 15 12  1  0  0  0  0
 15 16  1  1  0  0  0
 17 13  1  0  0  0  0
 18  8  1  0  0  0  0
 19  9  1  0  0  0  0
 20 10  2  0  0  0  0
 11 21  1  6  0  0  0
 12 22  1  1  0  0  0
 13 23  1  1  0  0  0
 24 16  2  0  0  0  0
 25 16  1  0  0  0  0
 26  7  1  0  0  0  0
 26 10  1  0  0  0  0
 27 14  1  0  0  0  0
 17 27  1  6  0  0  0
 28 15  1  0  0  0  0
 28 17  1  0  0  0  0
 29  7  1  0  0  0  0
 11 30  1  1  0  0  0
 12 31  1  6  0  0  0
 13 32  1  6  0  0  0
 15 33  1  1  0  0  0
 17 34  1  1  0  0  0
M  END
Download

3D MOL for HMDB0059986 (5-(3',4',5'-Trihydroxyphenyl)-gamma-valerolactone-4'-O-glucuronide)

HMDB0059986
     RDKit          3D
5-(3',4',5'-Trihydroxyphenyl)-gamma-valerolactone-4'-O-glucuronide
 48 50  0  0  0  0  0  0  0  0999 V2000
    6.1277    1.8965    2.2147 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8253    1.0222    1.3654 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7567   -0.0187    0.8577 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2398   -0.2353   -0.5432 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7567    0.0492   -0.4345 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0481   -1.2861   -0.3246 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5751   -1.1300   -0.2121 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9353   -1.0067    1.0042 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5674   -0.8626    1.0911 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0433   -0.7419    2.3162 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2400   -0.8338   -0.0410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6048   -0.6912    0.0272 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3124    0.5345    0.0352 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9608    0.7815    1.2025 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2867    0.3927    1.2838 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.4759   -1.0597    1.4315 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4920   -1.8164    1.4748 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7458   -1.5731    1.5213 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1247    0.9918    0.1736 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.1184    1.8369    0.6518 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2533    1.6944   -0.8482 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.9614    2.0982   -1.9539 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1537    0.7169   -1.2007 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4382    1.3147   -2.2366 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4044   -0.9575   -1.2517 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3367   -0.9380   -2.4261 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7825   -1.1027   -1.3406 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6219    0.8174    0.7251 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6589   -0.9726    1.4187 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8085    0.3378    0.8755 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6891    0.4875   -1.2508 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4141   -1.2929   -0.8799 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3737    0.5717   -1.3420 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3424   -1.9783   -1.1336 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3970   -1.7497    0.6240 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5726   -1.0295    1.8963 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5248   -0.7602    3.1510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5011    1.3222   -0.0409 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6797    0.8545    2.2339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1394   -2.0508    0.7169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6263    0.1559   -0.3549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8299    1.8967   -0.0366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7619    2.5798   -0.3901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2403    3.0592   -1.8479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5537   -0.2409   -1.5870 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9416    1.1435   -3.0690 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1065   -1.0265   -3.3298 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2935   -1.2008   -2.3039 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
  9 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  2  0
 16 18  1  0
 15 19  1  0
 19 20  1  0
 19 21  1  0
 21 22  1  0
 21 23  1  0
 23 24  1  0
 11 25  1  0
 25 26  1  0
 25 27  2  0
  5 28  1  0
 28  2  1  0
 27  7  1  0
 23 13  1  0
  3 29  1  0
  3 30  1  0
  4 31  1  0
  4 32  1  0
  5 33  1  0
  6 34  1  0
  6 35  1  0
  8 36  1  0
 10 37  1  0
 13 38  1  6
 15 39  1  1
 18 40  1  0
 19 41  1  6
 20 42  1  0
 21 43  1  1
 22 44  1  0
 23 45  1  6
 24 46  1  0
 26 47  1  0
 27 48  1  0
M  END
Download

3D SDF for HMDB0059986 (5-(3',4',5'-Trihydroxyphenyl)-gamma-valerolactone-4'-O-glucuronide)

  Mrv1652303102016572D          

 34 36  0  0  1  0            999 V2000
    2.9049    5.4562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1599    4.6715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    6.7661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    8.0036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    6.7661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    7.1786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    5.9411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    8.4161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    7.1786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9849    4.6715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   10.4786    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.4302   10.8911    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.1447    9.6536    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.7158    8.0036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   10.4786    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0013   10.8911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    9.2411    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.0013    9.2411    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    6.7661    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4698    4.0041    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   10.8911    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   11.7161    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592    9.2411    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   10.4786    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   11.7161    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2398    5.4562    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    8.4161    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    9.6536    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3074    6.3156    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   11.3036    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   11.3036    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    8.8286    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   10.0661    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    8.8286    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  6  3  1  0  0  0  0
  6  4  2  0  0  0  0
  6  5  1  0  0  0  0
  7  1  1  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
  9  5  2  0  0  0  0
 10  2  1  0  0  0  0
 12 11  1  0  0  0  0
 13 11  1  0  0  0  0
 14  8  2  0  0  0  0
 14  9  1  0  0  0  0
 15 12  1  0  0  0  0
 15 16  1  1  0  0  0
 17 13  1  0  0  0  0
 18  8  1  0  0  0  0
 19  9  1  0  0  0  0
 20 10  2  0  0  0  0
 11 21  1  6  0  0  0
 12 22  1  1  0  0  0
 13 23  1  1  0  0  0
 24 16  2  0  0  0  0
 25 16  1  0  0  0  0
 26  7  1  0  0  0  0
 26 10  1  0  0  0  0
 27 14  1  0  0  0  0
 17 27  1  6  0  0  0
 28 15  1  0  0  0  0
 28 17  1  0  0  0  0
 29  7  1  0  0  0  0
 11 30  1  1  0  0  0
 12 31  1  6  0  0  0
 13 32  1  6  0  0  0
 15 33  1  1  0  0  0
 17 34  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0059986

> <DATABASE_NAME>
hmdb

> <SMILES>
[H]C1(CC2=CC(O)=C(O[C@]3([H])O[C@]([H])(C(O)=O)[C@@]([H])(O)[C@]([H])(O)[C@@]3([H])O)C(O)=C2)CCC(=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C17H20O11/c18-8-4-6(3-7-1-2-10(20)26-7)5-9(19)14(8)27-17-13(23)11(21)12(22)15(28-17)16(24)25/h4-5,7,11-13,15,17-19,21-23H,1-3H2,(H,24,25)/t7?,11-,12-,13+,15-,17+/m0/s1

> <INCHI_KEY>
ATYNVCXMADLPJQ-YSVLGHOVSA-N

> <FORMULA>
C17H20O11

> <MOLECULAR_WEIGHT>
400.3341

> <EXACT_MASS>
400.100561482

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
48

> <JCHEM_AVERAGE_POLARIZABILITY>
37.10077531530408

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,4S,5R,6S)-6-{2,6-dihydroxy-4-[(5-oxooxolan-2-yl)methyl]phenoxy}-3,4,5-trihydroxyoxane-2-carboxylic acid

> <ALOGPS_LOGP>
0.06

> <JCHEM_LOGP>
-0.6360368223333333

> <ALOGPS_LOGS>
-1.72

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.54800854710895

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.895451756195147

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6868291978989394

> <JCHEM_POLAR_SURFACE_AREA>
183.21

> <JCHEM_REFRACTIVITY>
87.3004

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.70e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S,4S,5R,6S)-6-{2,6-dihydroxy-4-[(5-oxooxolan-2-yl)methyl]phenoxy}-3,4,5-trihydroxyoxane-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0059986 (5-(3',4',5'-Trihydroxyphenyl)-gamma-valerolactone-4'-O-glucuronide)

HMDB0059986
     RDKit          3D
5-(3',4',5'-Trihydroxyphenyl)-gamma-valerolactone-4'-O-glucuronide
 48 50  0  0  0  0  0  0  0  0999 V2000
    6.1277    1.8965    2.2147 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8253    1.0222    1.3654 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7567   -0.0187    0.8577 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2398   -0.2353   -0.5432 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7567    0.0492   -0.4345 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0481   -1.2861   -0.3246 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5751   -1.1300   -0.2121 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9353   -1.0067    1.0042 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5674   -0.8626    1.0911 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0433   -0.7419    2.3162 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2400   -0.8338   -0.0410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6048   -0.6912    0.0272 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3124    0.5345    0.0352 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9608    0.7815    1.2025 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2867    0.3927    1.2838 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.4759   -1.0597    1.4315 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4920   -1.8164    1.4748 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7458   -1.5731    1.5213 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1247    0.9918    0.1736 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.1184    1.8369    0.6518 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2533    1.6944   -0.8482 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.9614    2.0982   -1.9539 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1537    0.7169   -1.2007 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4382    1.3147   -2.2366 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4044   -0.9575   -1.2517 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3367   -0.9380   -2.4261 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7825   -1.1027   -1.3406 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6219    0.8174    0.7251 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6589   -0.9726    1.4187 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8085    0.3378    0.8755 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6891    0.4875   -1.2508 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4141   -1.2929   -0.8799 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3737    0.5717   -1.3420 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3424   -1.9783   -1.1336 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3970   -1.7497    0.6240 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5726   -1.0295    1.8963 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5248   -0.7602    3.1510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5011    1.3222   -0.0409 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6797    0.8545    2.2339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1394   -2.0508    0.7169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6263    0.1559   -0.3549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8299    1.8967   -0.0366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7619    2.5798   -0.3901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2403    3.0592   -1.8479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5537   -0.2409   -1.5870 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9416    1.1435   -3.0690 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1065   -1.0265   -3.3298 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2935   -1.2008   -2.3039 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
  9 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  2  0
 16 18  1  0
 15 19  1  0
 19 20  1  0
 19 21  1  0
 21 22  1  0
 21 23  1  0
 23 24  1  0
 11 25  1  0
 25 26  1  0
 25 27  2  0
  5 28  1  0
 28  2  1  0
 27  7  1  0
 23 13  1  0
  3 29  1  0
  3 30  1  0
  4 31  1  0
  4 32  1  0
  5 33  1  0
  6 34  1  0
  6 35  1  0
  8 36  1  0
 10 37  1  0
 13 38  1  6
 15 39  1  1
 18 40  1  0
 19 41  1  6
 20 42  1  0
 21 43  1  1
 22 44  1  0
 23 45  1  6
 24 46  1  0
 26 47  1  0
 27 48  1  0
M  END
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PDB for HMDB0059986 (5-(3',4',5'-Trihydroxyphenyl)-gamma-valerolactone-4'-O-glucuronide)

HEADER    PROTEIN                                 10-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-MAR-20         0                                  
HETATM    1  C   UNK     0       5.422  10.185   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.898   8.720   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.668  12.630   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.002  14.940   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.336  12.630   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.002  13.400   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.668  11.090   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.336  15.710   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      10.669  13.400   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.438   8.720   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      13.337  19.560   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.003  20.330   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      13.337  18.020   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.669  14.940   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      10.669  19.560   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.336  20.330   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      12.003  17.250   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       9.336  17.250   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      12.003  12.630   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       8.344   7.474   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      14.671  20.330   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      12.003  21.870   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      14.671  17.250   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       8.002  19.560   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       9.336  21.870   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       7.914  10.185   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      12.003  15.710   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      10.669  18.020   0.000  0.00  0.00           O+0
HETATM   29  H   UNK     0       8.040  11.789   0.000  0.00  0.00           H+0
HETATM   30  H   UNK     0      13.337  21.100   0.000  0.00  0.00           H+0
HETATM   31  H   UNK     0      10.669  21.100   0.000  0.00  0.00           H+0
HETATM   32  H   UNK     0      13.337  16.480   0.000  0.00  0.00           H+0
HETATM   33  H   UNK     0      12.003  18.790   0.000  0.00  0.00           H+0
HETATM   34  H   UNK     0      10.669  16.480   0.000  0.00  0.00           H+0
CONECT    1    2    7                                                       
CONECT    2    1   10                                                       
CONECT    3    6    7                                                       
CONECT    4    6    8                                                       
CONECT    5    6    9                                                       
CONECT    6    3    4    5                                                  
CONECT    7    1    3   26   29                                             
CONECT    8    4   14   18                                                  
CONECT    9    5   14   19                                                  
CONECT   10    2   20   26                                                  
CONECT   11   12   13   21   30                                             
CONECT   12   11   15   22   31                                             
CONECT   13   11   17   23   32                                             
CONECT   14    8    9   27                                                  
CONECT   15   12   16   28   33                                             
CONECT   16   15   24   25                                                  
CONECT   17   13   27   28   34                                             
CONECT   18    8                                                            
CONECT   19    9                                                            
CONECT   20   10                                                            
CONECT   21   11                                                            
CONECT   22   12                                                            
CONECT   23   13                                                            
CONECT   24   16                                                            
CONECT   25   16                                                            
CONECT   26    7   10                                                       
CONECT   27   14   17                                                       
CONECT   28   15   17                                                       
CONECT   29    7                                                            
CONECT   30   11                                                            
CONECT   31   12                                                            
CONECT   32   13                                                            
CONECT   33   15                                                            
CONECT   34   17                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   72    0
END
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3D PDB for HMDB0059986 (5-(3',4',5'-Trihydroxyphenyl)-gamma-valerolactone-4'-O-glucuronide)

COMPND    HMDB0059986
HETATM    1  O1  UNL     1       6.128   1.896   2.215  1.00  0.00           O  
HETATM    2  C1  UNL     1       5.825   1.022   1.365  1.00  0.00           C  
HETATM    3  C2  UNL     1       6.757  -0.019   0.858  1.00  0.00           C  
HETATM    4  C3  UNL     1       6.240  -0.235  -0.543  1.00  0.00           C  
HETATM    5  C4  UNL     1       4.757   0.049  -0.435  1.00  0.00           C  
HETATM    6  C5  UNL     1       4.048  -1.286  -0.325  1.00  0.00           C  
HETATM    7  C6  UNL     1       2.575  -1.130  -0.212  1.00  0.00           C  
HETATM    8  C7  UNL     1       1.935  -1.007   1.004  1.00  0.00           C  
HETATM    9  C8  UNL     1       0.567  -0.863   1.091  1.00  0.00           C  
HETATM   10  O2  UNL     1      -0.043  -0.742   2.316  1.00  0.00           O  
HETATM   11  C9  UNL     1      -0.240  -0.834  -0.041  1.00  0.00           C  
HETATM   12  O3  UNL     1      -1.605  -0.691   0.027  1.00  0.00           O  
HETATM   13  C10 UNL     1      -2.312   0.535   0.035  1.00  0.00           C  
HETATM   14  O4  UNL     1      -2.961   0.781   1.203  1.00  0.00           O  
HETATM   15  C11 UNL     1      -4.287   0.393   1.284  1.00  0.00           C  
HETATM   16  C12 UNL     1      -4.476  -1.060   1.432  1.00  0.00           C  
HETATM   17  O5  UNL     1      -3.492  -1.816   1.475  1.00  0.00           O  
HETATM   18  O6  UNL     1      -5.746  -1.573   1.521  1.00  0.00           O  
HETATM   19  C13 UNL     1      -5.125   0.992   0.174  1.00  0.00           C  
HETATM   20  O7  UNL     1      -6.118   1.837   0.652  1.00  0.00           O  
HETATM   21  C14 UNL     1      -4.253   1.694  -0.848  1.00  0.00           C  
HETATM   22  O8  UNL     1      -4.961   2.098  -1.954  1.00  0.00           O  
HETATM   23  C15 UNL     1      -3.154   0.717  -1.201  1.00  0.00           C  
HETATM   24  O9  UNL     1      -2.438   1.315  -2.237  1.00  0.00           O  
HETATM   25  C16 UNL     1       0.404  -0.957  -1.252  1.00  0.00           C  
HETATM   26  O10 UNL     1      -0.337  -0.938  -2.426  1.00  0.00           O  
HETATM   27  C17 UNL     1       1.783  -1.103  -1.341  1.00  0.00           C  
HETATM   28  O11 UNL     1       4.622   0.817   0.725  1.00  0.00           O  
HETATM   29  H1  UNL     1       6.659  -0.973   1.419  1.00  0.00           H  
HETATM   30  H2  UNL     1       7.809   0.338   0.875  1.00  0.00           H  
HETATM   31  H3  UNL     1       6.689   0.488  -1.251  1.00  0.00           H  
HETATM   32  H4  UNL     1       6.414  -1.293  -0.880  1.00  0.00           H  
HETATM   33  H5  UNL     1       4.374   0.572  -1.342  1.00  0.00           H  
HETATM   34  H6  UNL     1       4.342  -1.978  -1.134  1.00  0.00           H  
HETATM   35  H7  UNL     1       4.397  -1.750   0.624  1.00  0.00           H  
HETATM   36  H8  UNL     1       2.573  -1.029   1.896  1.00  0.00           H  
HETATM   37  H9  UNL     1       0.525  -0.760   3.151  1.00  0.00           H  
HETATM   38  H10 UNL     1      -1.501   1.322  -0.041  1.00  0.00           H  
HETATM   39  H11 UNL     1      -4.680   0.854   2.234  1.00  0.00           H  
HETATM   40  H12 UNL     1      -6.139  -2.051   0.717  1.00  0.00           H  
HETATM   41  H13 UNL     1      -5.626   0.156  -0.355  1.00  0.00           H  
HETATM   42  H14 UNL     1      -6.830   1.897  -0.037  1.00  0.00           H  
HETATM   43  H15 UNL     1      -3.762   2.580  -0.390  1.00  0.00           H  
HETATM   44  H16 UNL     1      -5.240   3.059  -1.848  1.00  0.00           H  
HETATM   45  H17 UNL     1      -3.554  -0.241  -1.587  1.00  0.00           H  
HETATM   46  H18 UNL     1      -2.942   1.144  -3.069  1.00  0.00           H  
HETATM   47  H19 UNL     1       0.107  -1.026  -3.330  1.00  0.00           H  
HETATM   48  H20 UNL     1       2.293  -1.201  -2.304  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   28
CONECT    3    4   29   30
CONECT    4    5   31   32
CONECT    5    6   28   33
CONECT    6    7   34   35
CONECT    7    8    8   27
CONECT    8    9   36
CONECT    9   10   11   11
CONECT   10   37
CONECT   11   12   25
CONECT   12   13
CONECT   13   14   23   38
CONECT   14   15
CONECT   15   16   19   39
CONECT   16   17   17   18
CONECT   18   40
CONECT   19   20   21   41
CONECT   20   42
CONECT   21   22   23   43
CONECT   22   44
CONECT   23   24   45
CONECT   24   46
CONECT   25   26   27   27
CONECT   26   47
CONECT   27   48
END
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SMILES for HMDB0059986 (5-(3',4',5'-Trihydroxyphenyl)-gamma-valerolactone-4'-O-glucuronide)

[H]C1(CC2=CC(O)=C(O[C@]3([H])O[C@]([H])(C(O)=O)[C@@]([H])(O)[C@]([H])(O)[C@@]3([H])O)C(O)=C2)CCC(=O)O1
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INCHI for HMDB0059986 (5-(3',4',5'-Trihydroxyphenyl)-gamma-valerolactone-4'-O-glucuronide)

InChI=1S/C17H20O11/c18-8-4-6(3-7-1-2-10(20)26-7)5-9(19)14(8)27-17-13(23)11(21)12(22)15(28-17)16(24)25/h4-5,7,11-13,15,17-19,21-23H,1-3H2,(H,24,25)/t7?,11-,12-,13+,15-,17+/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
5-(3',4',5'-Trihydroxyphenyl)-g-valerolactone-4'-O-glucuronideGenerator
5-(3',4',5'-Trihydroxyphenyl)-γ-valerolactone-4'-O-glucuronideGenerator
(2S,3S,4S,5R,6S)-6-{2,6-dihydroxy-4-[(5-oxooxolan-2-yl)methyl]phenoxy}-3,4,5-trihydroxyoxane-2-carboxylateGenerator
Chemical FormulaC17H20O11
Average Molecular Weight400.3341
Monoisotopic Molecular Weight400.100561482
IUPAC Name(2S,3S,4S,5R,6S)-6-{2,6-dihydroxy-4-[(5-oxooxolan-2-yl)methyl]phenoxy}-3,4,5-trihydroxyoxane-2-carboxylic acid
Traditional Name(2S,3S,4S,5R,6S)-6-{2,6-dihydroxy-4-[(5-oxooxolan-2-yl)methyl]phenoxy}-3,4,5-trihydroxyoxane-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
O[C@@H]1[C@@H](O)[C@H](OC2=C(O)C=C(CC3CCC(=O)O3)C=C2O)O[C@@H]([C@H]1O)C(O)=O
InChI Identifier
InChI=1S/C17H20O11/c18-8-4-6(3-7-1-2-10(20)26-7)5-9(19)14(8)27-17-13(23)11(21)12(22)15(28-17)16(24)25/h4-5,7,11-13,15,17-19,21-23H,1-3H2,(H,24,25)/t7?,11-,12-,13+,15-,17+/m0/s1
InChI KeyATYNVCXMADLPJQ-YSVLGHOVSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPhenolic glycosides
Alternative Parents
Substituents
  • Phenolic glycoside
  • Fatty acyl glycoside
  • Fatty acyl glycoside of mono- or disaccharide
  • 1-o-glucuronide
  • O-glucuronide
  • Glucuronic acid or derivatives
  • Alkyl glycoside
  • O-glycosyl compound
  • Phenoxy compound
  • Resorcinol
  • Phenol ether
  • 1-hydroxy-4-unsubstituted benzenoid
  • 1-hydroxy-2-unsubstituted benzenoid
  • Beta-hydroxy acid
  • Phenol
  • Gamma butyrolactone
  • Pyran
  • Oxane
  • Benzenoid
  • Dicarboxylic acid or derivatives
  • Fatty acyl
  • Monosaccharide
  • Monocyclic benzene moiety
  • Hydroxy acid
  • Tetrahydrofuran
  • Secondary alcohol
  • Carboxylic acid ester
  • Lactone
  • Polyol
  • Acetal
  • Organoheterocyclic compound
  • Carboxylic acid
  • Carboxylic acid derivative
  • Oxacycle
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic oxide
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue Locations
  • Kidney
  • Liver
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableNormal
      Not Available
 details
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)MaleNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB093658
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound124202074
PDB IDNot Available
ChEBI ID88692
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. van der Hooft JJ, de Vos RC, Mihaleva V, Bino RJ, Ridder L, de Roo N, Jacobs DM, van Duynhoven JP, Vervoort J: Structural elucidation and quantification of phenolic conjugates present in human urine after tea intake. Anal Chem. 2012 Aug 21;84(16):7263-71. doi: 10.1021/ac3017339. Epub 2012 Aug 2. [PubMed:22827565 ]