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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 20:30:35 UTC

Update Date

2022-03-07 02:54:32 UTC

HMDB ID

HMDB0035502

Secondary Accession Numbers

HMDB35502

Metabolite Identification

Common Name

Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer)

Description

Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer) belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group. Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer) has been detected, but not quantified in, fruits. This could make sambucus nigra degraded cyanogenic glycosides (2'-epimer) a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer).

Structure

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

HMDB0035502
     RDKit          3D
Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer)
 44 44  0  0  0  0  0  0  0  0999 V2000
    5.7004    1.3588   -0.4663 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4677    1.5918    0.1881 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4160    0.6565    0.1487 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6549   -0.3870   -0.5041 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1449    0.9453    0.8490 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5351    1.0779    2.3242 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4191    2.1561    2.4005 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2735   -0.0863    0.6424 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0796    0.2219    0.0488 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0297   -0.1963    0.7567 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9348    0.8010    1.0453 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9079    0.9751    2.5207 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8979    1.0932    3.6643 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2919    0.5544    0.5568 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0203    1.5194   -0.0743 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2880    1.2674   -0.5233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8269    0.0143   -0.3289 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1325   -0.9952    0.3029 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8600   -0.6839    0.7340 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0391   -0.4662   -1.2939 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0733   -0.0293   -2.1136 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0821   -1.9388   -1.1721 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7503   -2.5528   -0.4850 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0659   -2.6618   -1.8327 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1096   -4.0701   -1.7182 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9467    0.2787   -0.3877 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4755    1.9667    0.0678 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6663    1.6290   -1.5376 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7583    1.9002    0.4637 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6722    1.2187    2.9699 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1051    0.1618    2.5918 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9616    2.9299    2.7984 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0456    1.3252   -0.1706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5882    1.7761    0.6419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6048    2.5120   -0.2331 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8821    2.0521   -1.0373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8497   -0.1785   -0.6947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5776   -1.9893    0.4497 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2948   -1.4822    1.2403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9118   -0.1515   -1.8157 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5949   -0.7954   -2.4186 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6863   -4.3832   -0.8323 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6249   -4.5056   -2.6002 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0507   -4.4298   -1.6786 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  5  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  3  0
 11 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
  9 20  1  0
 20 21  1  0
 20 22  1  0
 22 23  2  0
 22 24  1  0
 24 25  1  0
 19 14  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  5 29  1  0
  6 30  1  0
  6 31  1  0
  7 32  1  0
  9 33  1  0
 11 34  1  6
 15 35  1  0
 16 36  1  0
 17 37  1  0
 18 38  1  0
 19 39  1  0
 20 40  1  0
 21 41  1  0
 25 42  1  0
 25 43  1  0
 25 44  1  0
M  END

  Mrv0541 10291206572D          

 25 25  0  0  0  0            999 V2000
   -0.1473   -4.6740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5671   -5.0865    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5672   -5.9115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1473   -6.3240    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8618   -5.9115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8618   -5.0865    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5762   -6.3240    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2907   -5.9115    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0052   -6.3240    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7197   -5.9115    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4341   -6.3240    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1486   -5.9115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8631   -6.3240    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5775   -5.9115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1486   -5.0865    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4341   -7.1490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1486   -7.5615    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0052   -7.1490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7197   -7.5615    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2907   -7.5615    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7197   -8.3865    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4341   -8.7990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0052   -7.9740    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5762   -7.1490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9929   -7.7324    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  1  6  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  6  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 12 15  2  0  0  0  0
 11 16  1  1  0  0  0
 16 17  1  0  0  0  0
  9 18  1  0  0  0  0
 18 19  1  6  0  0  0
 18 20  1  1  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 19 23  2  0  0  0  0
  7 24  1  1  0  0  0
 24 25  3  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0035502

> <DATABASE_NAME>
hmdb

> <SMILES>
COC(=O)C(CO)OC(O[C@H](C#N)C1=CC=CC=C1)C(O)C(=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C16H19NO8/c1-22-14(20)12(9-18)25-16(13(19)15(21)23-2)24-11(8-17)10-6-4-3-5-7-10/h3-7,11-13,16,18-19H,9H2,1-2H3/t11-,12?,13?,16?/m1/s1

> <INCHI_KEY>
BQIOAYLGMWMRRP-MPXNVAGNSA-N

> <FORMULA>
C16H19NO8

> <MOLECULAR_WEIGHT>
353.324

> <EXACT_MASS>
353.111066589

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
33.6108401665217

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl 3-[(S)-cyano(phenyl)methoxy]-2-hydroxy-3-[(3-hydroxy-1-methoxy-1-oxopropan-2-yl)oxy]propanoate

> <ALOGPS_LOGP>
0.51

> <JCHEM_LOGP>
0.16727685700000022

> <ALOGPS_LOGS>
-2.55

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.329165573155937

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.976175726113413

> <JCHEM_PKA_STRONGEST_BASIC>
-3.049837364232684

> <JCHEM_POLAR_SURFACE_AREA>
135.31

> <JCHEM_REFRACTIVITY>
81.998

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.00e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl 3-[(S)-cyano(phenyl)methoxy]-2-hydroxy-3-[(3-hydroxy-1-methoxy-1-oxopropan-2-yl)oxy]propanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0035502
     RDKit          3D
Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer)
 44 44  0  0  0  0  0  0  0  0999 V2000
    5.7004    1.3588   -0.4663 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4677    1.5918    0.1881 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4160    0.6565    0.1487 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6549   -0.3870   -0.5041 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1449    0.9453    0.8490 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5351    1.0779    2.3242 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4191    2.1561    2.4005 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2735   -0.0863    0.6424 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0796    0.2219    0.0488 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0297   -0.1963    0.7567 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9348    0.8010    1.0453 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9079    0.9751    2.5207 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8979    1.0932    3.6643 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2919    0.5544    0.5568 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0203    1.5194   -0.0743 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2880    1.2674   -0.5233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8269    0.0143   -0.3289 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1325   -0.9952    0.3029 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8600   -0.6839    0.7340 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0391   -0.4662   -1.2939 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0733   -0.0293   -2.1136 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0821   -1.9388   -1.1721 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7503   -2.5528   -0.4850 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0659   -2.6618   -1.8327 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1096   -4.0701   -1.7182 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9467    0.2787   -0.3877 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4755    1.9667    0.0678 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6663    1.6290   -1.5376 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7583    1.9002    0.4637 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6722    1.2187    2.9699 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1051    0.1618    2.5918 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9616    2.9299    2.7984 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0456    1.3252   -0.1706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5882    1.7761    0.6419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6048    2.5120   -0.2331 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8821    2.0521   -1.0373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8497   -0.1785   -0.6947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5776   -1.9893    0.4497 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2948   -1.4822    1.2403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9118   -0.1515   -1.8157 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5949   -0.7954   -2.4186 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6863   -4.3832   -0.8323 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6249   -4.5056   -2.6002 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0507   -4.4298   -1.6786 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  5  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  3  0
 11 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
  9 20  1  0
 20 21  1  0
 20 22  1  0
 22 23  2  0
 22 24  1  0
 24 25  1  0
 19 14  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  5 29  1  0
  6 30  1  0
  6 31  1  0
  7 32  1  0
  9 33  1  0
 11 34  1  6
 15 35  1  0
 16 36  1  0
 17 37  1  0
 18 38  1  0
 19 39  1  0
 20 40  1  0
 21 41  1  0
 25 42  1  0
 25 43  1  0
 25 44  1  0
M  END

HEADER    PROTEIN                                 29-OCT-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-OCT-12         0                                  
HETATM    1  C   UNK     0      -0.275  -8.725   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.059  -9.495   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.059 -11.035   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.275 -11.805   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.609 -11.035   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.609  -9.495   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.942 -11.805   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -4.276 -11.035   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -5.610 -11.805   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -6.943 -11.035   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -8.277 -11.805   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -9.611 -11.035   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0     -10.944 -11.805   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0     -12.278 -11.035   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -9.611  -9.495   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -8.277 -13.345   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -9.611 -14.115   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -5.610 -13.345   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -6.943 -14.115   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -4.276 -14.115   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -6.943 -15.655   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -8.277 -16.425   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -5.610 -14.885   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -2.942 -13.345   0.000  0.00  0.00           C+0
HETATM   25  N   UNK     0      -1.853 -14.434   0.000  0.00  0.00           N+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8   24                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   18                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   16                                                  
CONECT   12   11   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15   12                                                            
CONECT   16   11   17                                                       
CONECT   17   16                                                            
CONECT   18    9   19   20                                                  
CONECT   19   18   21   23                                                  
CONECT   20   18                                                            
CONECT   21   19   22                                                       
CONECT   22   21                                                            
CONECT   23   19                                                            
CONECT   24    7   25                                                       
CONECT   25   24                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   50    0
END

COMPND    HMDB0035502
HETATM    1  C1  UNL     1       5.700   1.359  -0.466  1.00  0.00           C  
HETATM    2  O1  UNL     1       4.468   1.592   0.188  1.00  0.00           O  
HETATM    3  C2  UNL     1       3.416   0.656   0.149  1.00  0.00           C  
HETATM    4  O2  UNL     1       3.655  -0.387  -0.504  1.00  0.00           O  
HETATM    5  C3  UNL     1       2.145   0.945   0.849  1.00  0.00           C  
HETATM    6  C4  UNL     1       2.535   1.078   2.324  1.00  0.00           C  
HETATM    7  O3  UNL     1       3.419   2.156   2.401  1.00  0.00           O  
HETATM    8  O4  UNL     1       1.274  -0.086   0.642  1.00  0.00           O  
HETATM    9  C5  UNL     1       0.080   0.222   0.049  1.00  0.00           C  
HETATM   10  O5  UNL     1      -1.030  -0.196   0.757  1.00  0.00           O  
HETATM   11  C6  UNL     1      -1.935   0.801   1.045  1.00  0.00           C  
HETATM   12  C7  UNL     1      -1.908   0.975   2.521  1.00  0.00           C  
HETATM   13  N1  UNL     1      -1.898   1.093   3.664  1.00  0.00           N  
HETATM   14  C8  UNL     1      -3.292   0.554   0.557  1.00  0.00           C  
HETATM   15  C9  UNL     1      -4.020   1.519  -0.074  1.00  0.00           C  
HETATM   16  C10 UNL     1      -5.288   1.267  -0.523  1.00  0.00           C  
HETATM   17  C11 UNL     1      -5.827   0.014  -0.329  1.00  0.00           C  
HETATM   18  C12 UNL     1      -5.132  -0.995   0.303  1.00  0.00           C  
HETATM   19  C13 UNL     1      -3.860  -0.684   0.734  1.00  0.00           C  
HETATM   20  C14 UNL     1       0.039  -0.466  -1.294  1.00  0.00           C  
HETATM   21  O6  UNL     1       1.073  -0.029  -2.114  1.00  0.00           O  
HETATM   22  C15 UNL     1       0.082  -1.939  -1.172  1.00  0.00           C  
HETATM   23  O7  UNL     1      -0.750  -2.553  -0.485  1.00  0.00           O  
HETATM   24  O8  UNL     1       1.066  -2.662  -1.833  1.00  0.00           O  
HETATM   25  C16 UNL     1       1.110  -4.070  -1.718  1.00  0.00           C  
HETATM   26  H1  UNL     1       5.947   0.279  -0.388  1.00  0.00           H  
HETATM   27  H2  UNL     1       6.475   1.967   0.068  1.00  0.00           H  
HETATM   28  H3  UNL     1       5.666   1.629  -1.538  1.00  0.00           H  
HETATM   29  H4  UNL     1       1.758   1.900   0.464  1.00  0.00           H  
HETATM   30  H5  UNL     1       1.672   1.219   2.970  1.00  0.00           H  
HETATM   31  H6  UNL     1       3.105   0.162   2.592  1.00  0.00           H  
HETATM   32  H7  UNL     1       2.962   2.930   2.798  1.00  0.00           H  
HETATM   33  H8  UNL     1       0.046   1.325  -0.171  1.00  0.00           H  
HETATM   34  H9  UNL     1      -1.588   1.776   0.642  1.00  0.00           H  
HETATM   35  H10 UNL     1      -3.605   2.512  -0.233  1.00  0.00           H  
HETATM   36  H11 UNL     1      -5.882   2.052  -1.037  1.00  0.00           H  
HETATM   37  H12 UNL     1      -6.850  -0.179  -0.695  1.00  0.00           H  
HETATM   38  H13 UNL     1      -5.578  -1.989   0.450  1.00  0.00           H  
HETATM   39  H14 UNL     1      -3.295  -1.482   1.240  1.00  0.00           H  
HETATM   40  H15 UNL     1      -0.912  -0.151  -1.816  1.00  0.00           H  
HETATM   41  H16 UNL     1       1.595  -0.795  -2.419  1.00  0.00           H  
HETATM   42  H17 UNL     1       1.686  -4.383  -0.832  1.00  0.00           H  
HETATM   43  H18 UNL     1       1.625  -4.506  -2.600  1.00  0.00           H  
HETATM   44  H19 UNL     1       0.051  -4.430  -1.679  1.00  0.00           H  
CONECT    1    2   26   27   28
CONECT    2    3
CONECT    3    4    4    5
CONECT    5    6    8   29
CONECT    6    7   30   31
CONECT    7   32
CONECT    8    9
CONECT    9   10   20   33
CONECT   10   11
CONECT   11   12   14   34
CONECT   12   13   13   13
CONECT   14   15   15   19
CONECT   15   16   35
CONECT   16   17   17   36
CONECT   17   18   37
CONECT   18   19   19   38
CONECT   19   39
CONECT   20   21   22   40
CONECT   21   41
CONECT   22   23   23   24
CONECT   24   25
CONECT   25   42   43   44
END

HMDB0035502
     RDKit          3D
Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer)
 44 44  0  0  0  0  0  0  0  0999 V2000
    5.7004    1.3588   -0.4663 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4677    1.5918    0.1881 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4160    0.6565    0.1487 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6549   -0.3870   -0.5041 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1449    0.9453    0.8490 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5351    1.0779    2.3242 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4191    2.1561    2.4005 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2735   -0.0863    0.6424 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0796    0.2219    0.0488 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0297   -0.1963    0.7567 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9348    0.8010    1.0453 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9079    0.9751    2.5207 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8979    1.0932    3.6643 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2919    0.5544    0.5568 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0203    1.5194   -0.0743 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2880    1.2674   -0.5233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8269    0.0143   -0.3289 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1325   -0.9952    0.3029 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8600   -0.6839    0.7340 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0391   -0.4662   -1.2939 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0733   -0.0293   -2.1136 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0821   -1.9388   -1.1721 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7503   -2.5528   -0.4850 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0659   -2.6618   -1.8327 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1096   -4.0701   -1.7182 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9467    0.2787   -0.3877 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4755    1.9667    0.0678 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6663    1.6290   -1.5376 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7583    1.9002    0.4637 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6722    1.2187    2.9699 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1051    0.1618    2.5918 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9616    2.9299    2.7984 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0456    1.3252   -0.1706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5882    1.7761    0.6419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6048    2.5120   -0.2331 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8821    2.0521   -1.0373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8497   -0.1785   -0.6947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5776   -1.9893    0.4497 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2948   -1.4822    1.2403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9118   -0.1515   -1.8157 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5949   -0.7954   -2.4186 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6863   -4.3832   -0.8323 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6249   -4.5056   -2.6002 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0507   -4.4298   -1.6786 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  5  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  3  0
 11 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
  9 20  1  0
 20 21  1  0
 20 22  1  0
 22 23  2  0
 22 24  1  0
 24 25  1  0
 19 14  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  5 29  1  0
  6 30  1  0
  6 31  1  0
  7 32  1  0
  9 33  1  0
 11 34  1  6
 15 35  1  0
 16 36  1  0
 17 37  1  0
 18 38  1  0
 19 39  1  0
 20 40  1  0
 21 41  1  0
 25 42  1  0
 25 43  1  0
 25 44  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Sambucus nigra degraded cyanogenic glycosides	HMDB
Methyl 3-[(S)-cyano(phenyl)methoxy]-2-hydroxy-3-[(3-hydroxy-1-methoxy-1-oxopropan-2-yl)oxy]propanoic acid	HMDB

Chemical Formula

C₁₆H₁₉NO₈

Average Molecular Weight

353.324

Monoisotopic Molecular Weight

353.111066589

IUPAC Name

methyl 3-[(S)-cyano(phenyl)methoxy]-2-hydroxy-3-[(3-hydroxy-1-methoxy-1-oxopropan-2-yl)oxy]propanoate

Traditional Name

methyl 3-[(S)-cyano(phenyl)methoxy]-2-hydroxy-3-[(3-hydroxy-1-methoxy-1-oxopropan-2-yl)oxy]propanoate

CAS Registry Number

Not Available

SMILES

COC(=O)C(CO)OC(O[C@H](C#N)C1=CC=CC=C1)C(O)C(=O)OC

InChI Identifier

InChI=1S/C16H19NO8/c1-22-14(20)12(9-18)25-16(13(19)15(21)23-2)24-11(8-17)10-6-4-3-5-7-10/h3-7,11-13,16,18-19H,9H2,1-2H3/t11-,12?,13?,16?/m1/s1

InChI Key

BQIOAYLGMWMRRP-MPXNVAGNSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Sugar acids and derivatives

Alternative Parents

Substituents

Beta-hydroxy acid
Glyceric_acid
Monocyclic benzene moiety
Dicarboxylic acid or derivatives
Benzenoid
Hydroxy acid
Monosaccharide
Methyl ester
Carboxylic acid ester
Secondary alcohol
Acetal
Carboxylic acid derivative
Carbonitrile
Nitrile
Hydrocarbon derivative
Organic oxide
Alcohol
Carbonyl group
Organopnictogen compound
Primary alcohol
Organonitrogen compound
Organic nitrogen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Exogenous (HMDB: HMDB0035502)

Food

Fruit

Fruits (FooDB: FOOD00871)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	1 g/L	ALOGPS
logP	0.51	ALOGPS
logP	0.17	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	10.98	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	135.31 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	82 m³·mol⁻¹	ChemAxon
Polarizability	33.61 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	182.084	31661259
DarkChem	[M-H]-	177.604	31661259
DeepCCS	[M+H]+	185.716	30932474
DeepCCS	[M-H]-	183.358	30932474
DeepCCS	[M-2H]-	216.959	30932474
DeepCCS	[M+Na]+	193.217	30932474
AllCCS	[M+H]+	181.3	32859911
AllCCS	[M+H-H2O]+	178.5	32859911
AllCCS	[M+NH4]+	183.8	32859911
AllCCS	[M+Na]+	184.5	32859911
AllCCS	[M-H]-	179.1	32859911
AllCCS	[M+Na-2H]-	179.4	32859911
AllCCS	[M+HCOO]-	179.8	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer)	COC(=O)C(CO)OC(O[C@H](C#N)C1=CC=CC=C1)C(O)C(=O)OC	2699.3	Standard polar	33892256
Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer)	COC(=O)C(CO)OC(O[C@H](C#N)C1=CC=CC=C1)C(O)C(=O)OC	2358.6	Standard non polar	33892256
Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer)	COC(=O)C(CO)OC(O[C@H](C#N)C1=CC=CC=C1)C(O)C(=O)OC	2376.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer),1TMS,isomer #1	COC(=O)C(CO[Si](C)(C)C)OC(O[C@H](C#N)C1=CC=CC=C1)C(O)C(=O)OC	2229.8	Semi standard non polar	33892256
Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer),1TMS,isomer #2	COC(=O)C(CO)OC(O[C@H](C#N)C1=CC=CC=C1)C(O[Si](C)(C)C)C(=O)OC	2220.7	Semi standard non polar	33892256
Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer),2TMS,isomer #1	COC(=O)C(CO[Si](C)(C)C)OC(O[C@H](C#N)C1=CC=CC=C1)C(O[Si](C)(C)C)C(=O)OC	2233.3	Semi standard non polar	33892256
Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer),1TBDMS,isomer #1	COC(=O)C(CO[Si](C)(C)C(C)(C)C)OC(O[C@H](C#N)C1=CC=CC=C1)C(O)C(=O)OC	2438.6	Semi standard non polar	33892256
Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer),1TBDMS,isomer #2	COC(=O)C(CO)OC(O[C@H](C#N)C1=CC=CC=C1)C(O[Si](C)(C)C(C)(C)C)C(=O)OC	2436.9	Semi standard non polar	33892256
Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer),2TBDMS,isomer #1	COC(=O)C(CO[Si](C)(C)C(C)(C)C)OC(O[C@H](C#N)C1=CC=CC=C1)C(O[Si](C)(C)C(C)(C)C)C(=O)OC	2644.5	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer) GC-MS (Non-derivatized) - 70eV, Positive	splash10-014i-3943000000-3342dd349fabde61dc13	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer) GC-MS (2 TMS) - 70eV, Positive	splash10-014i-3901400000-3178af70572123645000	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer) GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer) GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer) 10V, Positive-QTOF	splash10-0ff0-1912000000-0b8c168ef1e5b529b7f0	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer) 20V, Positive-QTOF	splash10-0fsi-1900000000-c84150550edd5fe663f4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer) 40V, Positive-QTOF	splash10-0pw9-5900000000-58dd969fa11453fc10cc	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer) 10V, Negative-QTOF	splash10-0ue9-4945000000-c70f85b40c7b1e33c205	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer) 20V, Negative-QTOF	splash10-001i-4911000000-08a562c914aeba0c7836	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer) 40V, Negative-QTOF	splash10-0a7r-9800000000-e8954c929c34b29e368c	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer) 10V, Positive-QTOF	splash10-014i-0900000000-de150ba28965ef39aa7a	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer) 20V, Positive-QTOF	splash10-014i-1910000000-06939fab88bd32147844	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer) 40V, Positive-QTOF	splash10-014i-7900000000-1d70f85f51723075d1b4	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer) 10V, Negative-QTOF	splash10-014i-2940000000-f2602c86cddcde8c2b0d	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer) 20V, Negative-QTOF	splash10-00lr-3900000000-48cce8d51ea41cf6a192	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer) 40V, Negative-QTOF	splash10-014i-2900000000-8597eefefd4cc3595a42	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB014190

KNApSAcK ID

Not Available

Chemspider ID

35013940

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

131751786

PDB ID

Not Available

ChEBI ID

168593

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer) (HMDB0035502)

MOL for HMDB0035502 (Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer))

3D MOL for HMDB0035502 (Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer))

3D SDF for HMDB0035502 (Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer))

3D-SDF for HMDB0035502 (Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer))

PDB for HMDB0035502 (Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer))

3D PDB for HMDB0035502 (Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer))

SMILES for HMDB0035502 (Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer))

INCHI for HMDB0035502 (Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer))

Structure for HMDB0035502 (Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer))

3D Structure for HMDB0035502 (Sambucus nigra Degraded cyanogenic glycosides (2'-Epimer))

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra