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Showing metabocard for pipecolic acid betaine (HMDB0304559)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-24 10:43:08 UTC
Update Date2022-09-22 18:35:14 UTC
HMDB IDHMDB0304559
Secondary Accession NumbersNone
Metabolite Identification
Common Namepipecolic acid betaine
Descriptionpipecolic acid betaine belongs to the class of organic compounds known as flavonoid-3-o-glycosides. These are phenolic compounds containing a flavonoid moiety which is O-glycosidically linked to carbohydrate moiety at the C3-position. pipecolic acid betaine has been detected, but not quantified in, several different foods, such as teffs (Eragrostis tef), triticales (X Triticosecale rimpaui), hard wheats (Triticum durum), amaranths (Amaranthus), and oriental wheats (Triticum turanicum). This could make pipecolic acid betaine a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on pipecolic acid betaine.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304559 (pipecolic acid betaine)


  Mrv1652308141918262D          

 31 34  0  0  1  0            999 V2000
    1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  2  1  0  0  0  0
  5  3  2  0  0  0  0
  8  1  1  1  0  0  0
  9  2  2  0  0  0  0
  9  3  1  0  0  0  0
 10  4  2  0  0  0  0
 10  5  1  0  0  0  0
 11  6  2  0  0  0  0
 11  7  1  0  0  0  0
 12  6  1  0  0  0  0
 13  7  2  0  0  0  0
 14 12  2  0  0  0  0
 14 13  1  0  0  0  0
 15  8  1  0  0  0  0
 16 14  1  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 19  9  1  0  0  0  0
 20 16  1  0  0  0  0
 20 19  2  0  0  0  0
 18 21  1  0  0  0  0
 22 10  1  0  0  0  0
 23 11  1  0  0  0  0
 24 12  1  0  0  0  0
 15 25  1  6  0  0  0
 26 16  2  0  0  0  0
 17 27  1  1  0  0  0
 18 28  1  1  0  0  0
  8 29  1  0  0  0  0
 29 21  1  0  0  0  0
 30 13  1  0  0  0  0
 30 19  1  0  0  0  0
 31 20  1  0  0  0  0
 31 21  1  0  0  0  0
M  END
Download

3D MOL for HMDB0304559 (pipecolic acid betaine)

HMDB0304559
     RDKit          3D
pipecolic acid betaine
 51 54  0  0  0  0  0  0  0  0999 V2000
    2.8404   -0.6805    1.7260 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1539   -1.1999    0.3133 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9646   -1.2644   -0.3485 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3899   -0.0775   -0.7121 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1486   -0.3310   -1.3723 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9736    0.2474   -0.8131 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7616   -0.4052    0.0361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6079   -1.7535    0.4785 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8247   -2.7109   -0.0689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7230   -3.9822    0.4845 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4045   -4.3607    1.6180 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2880   -5.6363    2.1537 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2073   -3.3955    2.1852 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3089   -2.1462    1.6447 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8072    0.2883    0.5184 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0488    1.5296    0.1779 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1529    2.1620    0.7287 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4480    3.4611    0.4031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5692    4.0920    0.9671 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6975    4.1939   -0.4577 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5625    3.5824   -1.0400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8010    4.3026   -1.9038 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2673    2.2544   -0.7024 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1865    1.5837   -1.2175 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4215    2.1349   -2.0140 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2785    0.6798   -1.6918 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5188    1.9342   -1.1559 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6389   -0.0121   -1.7669 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.5734    0.8235   -2.3743 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1079   -0.2932   -0.3772 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.4256   -0.7431   -0.3333 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7079    0.4232    1.5995 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6546   -0.9084    2.4224 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8634   -1.0875    2.0099 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5657   -2.2476    0.4274 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2145    0.5564    0.1762 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2862   -2.4778   -0.9845 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0756   -4.6858   -0.0136 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8217   -5.8361    2.9886 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7613   -3.6777    3.0917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9687   -1.4249    2.1509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7701    1.5941    1.4221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1461    3.5722    1.6107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9047    5.2094   -0.7297 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0120    4.0714   -2.3897 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8375    0.7844   -2.6800 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4300    2.2326   -1.4027 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5597   -0.9252   -2.3784 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0298    0.3700   -3.1308 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1056    0.6799    0.1707 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7992   -0.5002    0.5537 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  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 11 13  1  0
 13 14  2  0
  7 15  1  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  1  0
 18 20  2  0
 20 21  1  0
 21 22  1  0
 21 23  2  0
 23 24  1  0
 24 25  2  0
  4 26  1  0
 26 27  1  0
 26 28  1  0
 28 29  1  0
 28 30  1  0
 30 31  1  0
 30  2  1  0
 24  6  1  0
 14  8  1  0
 23 16  1  0
  1 32  1  0
  1 33  1  0
  1 34  1  0
  2 35  1  1
  4 36  1  0
  9 37  1  0
 10 38  1  0
 12 39  1  0
 13 40  1  0
 14 41  1  0
 17 42  1  0
 19 43  1  0
 20 44  1  0
 22 45  1  0
 26 46  1  6
 27 47  1  0
 28 48  1  6
 29 49  1  0
 30 50  1  1
 31 51  1  0
M  END
Download

3D SDF for HMDB0304559 (pipecolic acid betaine)


  Mrv1652308141918262D          

 31 34  0  0  1  0            999 V2000
    1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  2  1  0  0  0  0
  5  3  2  0  0  0  0
  8  1  1  1  0  0  0
  9  2  2  0  0  0  0
  9  3  1  0  0  0  0
 10  4  2  0  0  0  0
 10  5  1  0  0  0  0
 11  6  2  0  0  0  0
 11  7  1  0  0  0  0
 12  6  1  0  0  0  0
 13  7  2  0  0  0  0
 14 12  2  0  0  0  0
 14 13  1  0  0  0  0
 15  8  1  0  0  0  0
 16 14  1  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 19  9  1  0  0  0  0
 20 16  1  0  0  0  0
 20 19  2  0  0  0  0
 18 21  1  0  0  0  0
 22 10  1  0  0  0  0
 23 11  1  0  0  0  0
 24 12  1  0  0  0  0
 15 25  1  6  0  0  0
 26 16  2  0  0  0  0
 17 27  1  1  0  0  0
 18 28  1  1  0  0  0
  8 29  1  0  0  0  0
 29 21  1  0  0  0  0
 30 13  1  0  0  0  0
 30 19  1  0  0  0  0
 31 20  1  0  0  0  0
 31 21  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0304559

> <DATABASE_NAME>
hmdb

> <SMILES>
C[C@H]1OC(OC2=C(OC3=CC(O)=CC(O)=C3C2=O)C2=CC=C(O)C=C2)[C@@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C21H20O10/c1-8-15(25)17(27)18(28)21(29-8)31-20-16(26)14-12(24)6-11(23)7-13(14)30-19(20)9-2-4-10(22)5-3-9/h2-8,15,17-18,21-25,27-28H,1H3/t8-,15-,17+,18+,21?/m1/s1

> <INCHI_KEY>
SOSLMHZOJATCCP-VVTWGIOXSA-N

> <FORMULA>
C21H20O10

> <MOLECULAR_WEIGHT>
432.381

> <EXACT_MASS>
432.105646844

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
51

> <JCHEM_AVERAGE_POLARIZABILITY>
41.13089592641112

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5,7-dihydroxy-2-(4-hydroxyphenyl)-3-{[(3S,4S,5S,6R)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}-4H-chromen-4-one

> <ALOGPS_LOGP>
1.48

> <JCHEM_LOGP>
1.2056399923333339

> <ALOGPS_LOGS>
-2.45

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.869705133213711

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.372348629689458

> <JCHEM_PKA_STRONGEST_BASIC>
-3.612200408172593

> <JCHEM_POLAR_SURFACE_AREA>
166.14

> <JCHEM_REFRACTIVITY>
105.75089999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.55e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5,7-dihydroxy-2-(4-hydroxyphenyl)-3-{[(3S,4S,5S,6R)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}chromen-4-one

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0304559 (pipecolic acid betaine)

HMDB0304559
     RDKit          3D
pipecolic acid betaine
 51 54  0  0  0  0  0  0  0  0999 V2000
    2.8404   -0.6805    1.7260 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1539   -1.1999    0.3133 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9646   -1.2644   -0.3485 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3899   -0.0775   -0.7121 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1486   -0.3310   -1.3723 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9736    0.2474   -0.8131 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7616   -0.4052    0.0361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6079   -1.7535    0.4785 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8247   -2.7109   -0.0689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7230   -3.9822    0.4845 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4045   -4.3607    1.6180 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2880   -5.6363    2.1537 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2073   -3.3955    2.1852 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3089   -2.1462    1.6447 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8072    0.2883    0.5184 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0488    1.5296    0.1779 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1529    2.1620    0.7287 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4480    3.4611    0.4031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5692    4.0920    0.9671 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6975    4.1939   -0.4577 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5625    3.5824   -1.0400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8010    4.3026   -1.9038 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2673    2.2544   -0.7024 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1865    1.5837   -1.2175 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4215    2.1349   -2.0140 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2785    0.6798   -1.6918 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5188    1.9342   -1.1559 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6389   -0.0121   -1.7669 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.5734    0.8235   -2.3743 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1079   -0.2932   -0.3772 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.4256   -0.7431   -0.3333 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7079    0.4232    1.5995 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6546   -0.9084    2.4224 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8634   -1.0875    2.0099 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5657   -2.2476    0.4274 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2145    0.5564    0.1762 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2862   -2.4778   -0.9845 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0756   -4.6858   -0.0136 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8217   -5.8361    2.9886 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7613   -3.6777    3.0917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9687   -1.4249    2.1509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7701    1.5941    1.4221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1461    3.5722    1.6107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9047    5.2094   -0.7297 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0120    4.0714   -2.3897 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8375    0.7844   -2.6800 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4300    2.2326   -1.4027 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5597   -0.9252   -2.3784 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0298    0.3700   -3.1308 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1056    0.6799    0.1707 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7992   -0.5002    0.5537 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  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 11 13  1  0
 13 14  2  0
  7 15  1  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  1  0
 18 20  2  0
 20 21  1  0
 21 22  1  0
 21 23  2  0
 23 24  1  0
 24 25  2  0
  4 26  1  0
 26 27  1  0
 26 28  1  0
 28 29  1  0
 28 30  1  0
 30 31  1  0
 30  2  1  0
 24  6  1  0
 14  8  1  0
 23 16  1  0
  1 32  1  0
  1 33  1  0
  1 34  1  0
  2 35  1  1
  4 36  1  0
  9 37  1  0
 10 38  1  0
 12 39  1  0
 13 40  1  0
 14 41  1  0
 17 42  1  0
 19 43  1  0
 20 44  1  0
 22 45  1  0
 26 46  1  6
 27 47  1  0
 28 48  1  6
 29 49  1  0
 30 50  1  1
 31 51  1  0
M  END
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PDB for HMDB0304559 (pipecolic acid betaine)

HEADER    PROTEIN                                 14-AUG-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-AUG-19         0                                  
HETATM    1  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       5.335  -9.240   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       8.002  -7.700   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       8.002  -4.620   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       4.001  -5.390   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
CONECT    1    8                                                            
CONECT    2    4    9                                                       
CONECT    3    5    9                                                       
CONECT    4    2   10                                                       
CONECT    5    3   10                                                       
CONECT    6   11   12                                                       
CONECT    7   11   13                                                       
CONECT    8    1   15   29                                                  
CONECT    9    2    3   19                                                  
CONECT   10    4    5   22                                                  
CONECT   11    6    7   23                                                  
CONECT   12    6   14   24                                                  
CONECT   13    7   14   30                                                  
CONECT   14   12   13   16                                                  
CONECT   15    8   17   25                                                  
CONECT   16   14   20   26                                                  
CONECT   17   15   18   27                                                  
CONECT   18   17   21   28                                                  
CONECT   19    9   20   30                                                  
CONECT   20   16   19   31                                                  
CONECT   21   18   29   31                                                  
CONECT   22   10                                                            
CONECT   23   11                                                            
CONECT   24   12                                                            
CONECT   25   15                                                            
CONECT   26   16                                                            
CONECT   27   17                                                            
CONECT   28   18                                                            
CONECT   29    8   21                                                       
CONECT   30   13   19                                                       
CONECT   31   20   21                                                       
MASTER        0    0    0    0    0    0    0    0   31    0   68    0
END
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3D PDB for HMDB0304559 (pipecolic acid betaine)

COMPND    HMDB0304559
HETATM    1  C1  UNL     1       2.840  -0.681   1.726  1.00  0.00           C  
HETATM    2  C2  UNL     1       3.154  -1.200   0.313  1.00  0.00           C  
HETATM    3  O1  UNL     1       1.965  -1.264  -0.348  1.00  0.00           O  
HETATM    4  C3  UNL     1       1.390  -0.077  -0.712  1.00  0.00           C  
HETATM    5  O2  UNL     1       0.149  -0.331  -1.372  1.00  0.00           O  
HETATM    6  C4  UNL     1      -0.974   0.247  -0.813  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.762  -0.405   0.036  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.608  -1.753   0.478  1.00  0.00           C  
HETATM    9  C7  UNL     1      -0.825  -2.711  -0.069  1.00  0.00           C  
HETATM   10  C8  UNL     1      -0.723  -3.982   0.485  1.00  0.00           C  
HETATM   11  C9  UNL     1      -1.405  -4.361   1.618  1.00  0.00           C  
HETATM   12  O3  UNL     1      -1.288  -5.636   2.154  1.00  0.00           O  
HETATM   13  C10 UNL     1      -2.207  -3.396   2.185  1.00  0.00           C  
HETATM   14  C11 UNL     1      -2.309  -2.146   1.645  1.00  0.00           C  
HETATM   15  O4  UNL     1      -2.807   0.288   0.518  1.00  0.00           O  
HETATM   16  C12 UNL     1      -3.049   1.530   0.178  1.00  0.00           C  
HETATM   17  C13 UNL     1      -4.153   2.162   0.729  1.00  0.00           C  
HETATM   18  C14 UNL     1      -4.448   3.461   0.403  1.00  0.00           C  
HETATM   19  O5  UNL     1      -5.569   4.092   0.967  1.00  0.00           O  
HETATM   20  C15 UNL     1      -3.698   4.194  -0.458  1.00  0.00           C  
HETATM   21  C16 UNL     1      -2.563   3.582  -1.040  1.00  0.00           C  
HETATM   22  O6  UNL     1      -1.801   4.303  -1.904  1.00  0.00           O  
HETATM   23  C17 UNL     1      -2.267   2.254  -0.702  1.00  0.00           C  
HETATM   24  C18 UNL     1      -1.186   1.584  -1.217  1.00  0.00           C  
HETATM   25  O7  UNL     1      -0.421   2.135  -2.014  1.00  0.00           O  
HETATM   26  C19 UNL     1       2.279   0.680  -1.692  1.00  0.00           C  
HETATM   27  O8  UNL     1       2.519   1.934  -1.156  1.00  0.00           O  
HETATM   28  C20 UNL     1       3.639  -0.012  -1.767  1.00  0.00           C  
HETATM   29  O9  UNL     1       4.573   0.823  -2.374  1.00  0.00           O  
HETATM   30  C21 UNL     1       4.108  -0.293  -0.377  1.00  0.00           C  
HETATM   31  O10 UNL     1       5.426  -0.743  -0.333  1.00  0.00           O  
HETATM   32  H1  UNL     1       2.708   0.423   1.600  1.00  0.00           H  
HETATM   33  H2  UNL     1       3.655  -0.908   2.422  1.00  0.00           H  
HETATM   34  H3  UNL     1       1.863  -1.087   2.010  1.00  0.00           H  
HETATM   35  H4  UNL     1       3.566  -2.248   0.427  1.00  0.00           H  
HETATM   36  H5  UNL     1       1.214   0.556   0.176  1.00  0.00           H  
HETATM   37  H6  UNL     1      -0.286  -2.478  -0.984  1.00  0.00           H  
HETATM   38  H7  UNL     1      -0.076  -4.686  -0.014  1.00  0.00           H  
HETATM   39  H8  UNL     1      -1.822  -5.836   2.989  1.00  0.00           H  
HETATM   40  H9  UNL     1      -2.761  -3.678   3.092  1.00  0.00           H  
HETATM   41  H10 UNL     1      -2.969  -1.425   2.151  1.00  0.00           H  
HETATM   42  H11 UNL     1      -4.770   1.594   1.422  1.00  0.00           H  
HETATM   43  H12 UNL     1      -6.146   3.572   1.611  1.00  0.00           H  
HETATM   44  H13 UNL     1      -3.905   5.209  -0.730  1.00  0.00           H  
HETATM   45  H14 UNL     1      -1.012   4.071  -2.390  1.00  0.00           H  
HETATM   46  H15 UNL     1       1.837   0.784  -2.680  1.00  0.00           H  
HETATM   47  H16 UNL     1       3.430   2.233  -1.403  1.00  0.00           H  
HETATM   48  H17 UNL     1       3.560  -0.925  -2.378  1.00  0.00           H  
HETATM   49  H18 UNL     1       5.030   0.370  -3.131  1.00  0.00           H  
HETATM   50  H19 UNL     1       4.106   0.680   0.171  1.00  0.00           H  
HETATM   51  H20 UNL     1       5.799  -0.500   0.554  1.00  0.00           H  
CONECT    1    2   32   33   34
CONECT    2    3   30   35
CONECT    3    4
CONECT    4    5   26   36
CONECT    5    6
CONECT    6    7    7   24
CONECT    7    8   15
CONECT    8    9    9   14
CONECT    9   10   37
CONECT   10   11   11   38
CONECT   11   12   13
CONECT   12   39
CONECT   13   14   14   40
CONECT   14   41
CONECT   15   16
CONECT   16   17   17   23
CONECT   17   18   42
CONECT   18   19   20   20
CONECT   19   43
CONECT   20   21   44
CONECT   21   22   23   23
CONECT   22   45
CONECT   23   24
CONECT   24   25   25
CONECT   26   27   28   46
CONECT   27   47
CONECT   28   29   30   48
CONECT   29   49
CONECT   30   31   50
CONECT   31   51
END
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SMILES for HMDB0304559 (pipecolic acid betaine)

C[C@H]1OC(OC2=C(OC3=CC(O)=CC(O)=C3C2=O)C2=CC=C(O)C=C2)[C@@H](O)[C@@H](O)[C@@H]1O
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INCHI for HMDB0304559 (pipecolic acid betaine)

InChI=1S/C21H20O10/c1-8-15(25)17(27)18(28)21(29-8)31-20-16(26)14-12(24)6-11(23)7-13(14)30-19(20)9-2-4-10(22)5-3-9/h2-8,15,17-18,21-25,27-28H,1H3/t8-,15-,17+,18+,21?/m1/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Pipecolate betaineGenerator
Kaempferol 3-O-alpha-rhamnosideHMDB
Chemical FormulaC21H20O10
Average Molecular Weight432.381
Monoisotopic Molecular Weight432.105646844
IUPAC Name5,7-dihydroxy-2-(4-hydroxyphenyl)-3-{[(3S,4S,5S,6R)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}-4H-chromen-4-one
Traditional Name5,7-dihydroxy-2-(4-hydroxyphenyl)-3-{[(3S,4S,5S,6R)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}chromen-4-one
CAS Registry NumberNot Available
SMILES
C[C@H]1OC(OC2=C(OC3=CC(O)=CC(O)=C3C2=O)C2=CC=C(O)C=C2)[C@@H](O)[C@@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C21H20O10/c1-8-15(25)17(27)18(28)21(29-8)31-20-16(26)14-12(24)6-11(23)7-13(14)30-19(20)9-2-4-10(22)5-3-9/h2-8,15,17-18,21-25,27-28H,1H3/t8-,15-,17+,18+,21?/m1/s1
InChI KeySOSLMHZOJATCCP-VVTWGIOXSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as flavonoid-3-o-glycosides. These are phenolic compounds containing a flavonoid moiety which is O-glycosidically linked to carbohydrate moiety at the C3-position.
KingdomOrganic compounds
Super ClassPhenylpropanoids and polyketides
ClassFlavonoids
Sub ClassFlavonoid glycosides
Direct ParentFlavonoid-3-O-glycosides
Alternative Parents
Substituents
  • Flavonoid-3-o-glycoside
  • 4'-hydroxyflavonoid
  • 5-hydroxyflavonoid
  • 7-hydroxyflavonoid
  • Flavone
  • Hydroxyflavonoid
  • Hexose monosaccharide
  • Chromone
  • Glycosyl compound
  • O-glycosyl compound
  • Benzopyran
  • 1-benzopyran
  • 1-hydroxy-4-unsubstituted benzenoid
  • 1-hydroxy-2-unsubstituted benzenoid
  • Phenol
  • Pyranone
  • Pyran
  • Oxane
  • Monocyclic benzene moiety
  • Benzenoid
  • Monosaccharide
  • Heteroaromatic compound
  • Vinylogous acid
  • Secondary alcohol
  • Oxacycle
  • Polyol
  • Acetal
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organooxygen compound
  • Alcohol
  • Organic oxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
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
logP1.48ALOGPS
logP1.21ChemAxon
logS-2.4ALOGPS
pKa (Strongest Acidic)6.37ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area166.14 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity105.75 m³·mol⁻¹ChemAxon
Polarizability41.13 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+200.50132859911
AllCCS[M+H-H2O]+197.90932859911
AllCCS[M+Na]+203.5732859911
AllCCS[M+NH4]+202.88732859911
AllCCS[M-H]-198.63832859911
AllCCS[M+Na-2H]-198.78232859911
AllCCS[M+HCOO]-199.09632859911
DeepCCS[M+H]+191.89830932474
DeepCCS[M-H]-189.50230932474
DeepCCS[M-2H]-222.73230932474
DeepCCS[M+Na]+198.10230932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - pipecolic acid betaine 10V, Positive-QTOFsplash10-001i-0000900000-509ee28ef47ce2bd195a2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - pipecolic acid betaine 20V, Positive-QTOFsplash10-001i-0000900000-79f1f1320d12612412012021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - pipecolic acid betaine 40V, Positive-QTOFsplash10-0udi-1901400000-21936e8358041c3da9542021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - pipecolic acid betaine 10V, Negative-QTOFsplash10-001i-0000900000-14577e71d57aee3c040a2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - pipecolic acid betaine 20V, Negative-QTOFsplash10-0f89-0300900000-595fe4f85be7fec14af82021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - pipecolic acid betaine 40V, Negative-QTOFsplash10-0uec-2910200000-e575142d2a72f3f475222021-10-21Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedAdult (>18 years old)BothAsthma details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothAsthma details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB093496
KNApSAcK IDC00005140
Chemspider ID18583422
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound22838616
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