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Showing metabocard for 3''-deamino-3''-oxonicotianamine (HMDB0304096)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 07:08:44 UTC
Update Date2021-09-24 07:08:44 UTC
HMDB IDHMDB0304096
Secondary Accession NumbersNone
Metabolite Identification
Common Name3''-deamino-3''-oxonicotianamine
Description 3''-deamino-3''-oxonicotianamine is practically insoluble (in water) and a moderately acidic compound (based on its pKa). 3''-deamino-3''-oxonicotianamine can be found in a number of food items such as daikon radish, nutmeg, greenthread tea, and small-leaf linden, which makes 3''-deamino-3''-oxonicotianamine a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304096 (3''-deamino-3''-oxonicotianamine)


  Mrv1533005141512322D          

 21 21  0  0  0  0            999 V2000
    1.9093   -0.1428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9093   -0.9678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1948   -1.3803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4804   -0.9678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2341   -1.3803    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -0.4476   -2.1771    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2445   -1.9636    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0310   -1.1667    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0351   -2.8916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4476   -3.6061    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.7899   -2.8916    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6238   -1.3803    0.0000 N   0  3  0  0  0  2  0  0  0  0  0  0
    3.3383   -0.9678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0527   -1.3803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7672   -0.9678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4817   -1.3803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1961   -0.9678    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.4817   -2.2053    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7672   -0.1428    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6238    0.2697    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.1948    0.2697    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  5  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
  2 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  2  0  0  0  0
 15 19  2  0  0  0  0
  1 20  1  0  0  0  0
  1 21  2  0  0  0  0
M  CHG  5   5   1  10  -1  12   1  17  -1  20  -1
M  RAD  1   5   2
M  END
Download

3D MOL for HMDB0304096 (3''-deamino-3''-oxonicotianamine)

HMDB0304096
     RDKit          3D
3''-deamino-3''-oxonicotianamine
 35 35  0  0  0  0  0  0  0  0999 V2000
   -5.2580    0.2674   -1.4125 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5703   -0.7996   -0.8265 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9255   -1.0657   -0.6854 O   0  0  0  0  0  1  0  0  0  0  0  0
   -4.5338   -1.6792   -0.3378 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8542   -2.7366    0.2415 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1126   -1.3304   -0.5219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6169   -0.8103    0.8303 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2823   -0.4294    0.8559 N   0  0  0  0  0  2  0  0  0  0  0  0
   -0.8326    0.8604    0.5967 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2983    0.9090   -0.4543 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4660    0.1079    0.0418 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5882    0.0380   -0.7856 N   0  0  0  0  0  3  0  0  0  0  0  0
    3.4101    1.1440   -1.0585 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1417    0.8867    0.2394 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7271   -0.5509   -0.0645 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6788   -1.2668   -0.9164 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7080   -0.7167   -1.3746 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4510   -2.5900   -1.2351 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.7886    1.9223    0.3037 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9774    1.8294   -0.0150 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2969    3.2439    0.3938 O   0  0  0  0  0  1  0  0  0  0  0  0
   -2.5362   -2.2591   -0.7270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0322   -0.5880   -1.3167 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3782   -0.1050    1.2112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7287   -1.7117    1.5123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2963    1.2088    1.5388 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5064    1.9553   -0.6594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1497    0.4659   -1.3696 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0938   -0.9176    0.2573 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7244    0.5303    1.0594 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9976    2.1305   -1.2054 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1176    0.9101   -1.9082 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6278    1.2645    1.1279 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2292    1.0124    0.2099 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4042   -1.1302    0.8214 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
  9 19  1  0
 19 20  2  0
 19 21  1  0
 15 12  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
  9 26  1  0
 10 27  1  0
 10 28  1  0
 11 29  1  0
 11 30  1  0
 13 31  1  0
 13 32  1  0
 14 33  1  0
 14 34  1  0
 15 35  1  0
M  CHG  5   3  -1   8   1  12   1  18  -1  21  -1
M  RAD  2   8   3  12   2
M  END
Download

3D SDF for HMDB0304096 (3''-deamino-3''-oxonicotianamine)


  Mrv1533005141512322D          

 21 21  0  0  0  0            999 V2000
    1.9093   -0.1428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9093   -0.9678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1948   -1.3803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4804   -0.9678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2341   -1.3803    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -0.4476   -2.1771    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2445   -1.9636    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0310   -1.1667    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0351   -2.8916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4476   -3.6061    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.7899   -2.8916    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6238   -1.3803    0.0000 N   0  3  0  0  0  2  0  0  0  0  0  0
    3.3383   -0.9678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0527   -1.3803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7672   -0.9678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4817   -1.3803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1961   -0.9678    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.4817   -2.2053    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7672   -0.1428    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6238    0.2697    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.1948    0.2697    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  5  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
  2 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  2  0  0  0  0
 15 19  2  0  0  0  0
  1 20  1  0  0  0  0
  1 21  2  0  0  0  0
M  CHG  5   5   1  10  -1  12   1  17  -1  20  -1
M  RAD  1   5   2
M  END
> <DATABASE_ID>
HMDB0304096

> <DATABASE_NAME>
hmdb

> <SMILES>
[O-]C(=O)C(CC[N+]1CCC1C([O-])=O)[N+]CCC(=O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C12H17N2O7/c15-9(12(20)21)1-4-13-7(10(16)17)2-5-14-6-3-8(14)11(18)19/h7-8H,1-6H2,(H,16,17)(H,18,19)(H,20,21)/q+2/p-3

> <INCHI_KEY>
RPGJYKVCHUARBL-UHFFFAOYSA-K

> <FORMULA>
C12H14N2O7

> <MOLECULAR_WEIGHT>
298.252

> <EXACT_MASS>
298.080649379

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
27.451222323419763

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-carboxylato-1-{3-carboxylato-3-[(3-carboxylato-3-oxopropyl)azaniumyl]propyl}azetidin-1-ium-1-yl

> <ALOGPS_LOGP>
0.82

> <JCHEM_LOGP>
-2.3443289113476915

> <ALOGPS_LOGS>
-4.09

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
2.4444946119699864

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.757996186206745

> <JCHEM_PKA_STRONGEST_BASIC>
-9.783465740248136

> <JCHEM_POLAR_SURFACE_AREA>
160.28

> <JCHEM_REFRACTIVITY>
100.1754

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.47e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-carboxylato-1-{3-carboxylato-3-[(3-carboxylato-3-oxopropyl)ammonio]propyl}azetidin-1-ium-1-yl

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0304096 (3''-deamino-3''-oxonicotianamine)

HMDB0304096
     RDKit          3D
3''-deamino-3''-oxonicotianamine
 35 35  0  0  0  0  0  0  0  0999 V2000
   -5.2580    0.2674   -1.4125 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5703   -0.7996   -0.8265 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9255   -1.0657   -0.6854 O   0  0  0  0  0  1  0  0  0  0  0  0
   -4.5338   -1.6792   -0.3378 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8542   -2.7366    0.2415 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1126   -1.3304   -0.5219 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6169   -0.8103    0.8303 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2823   -0.4294    0.8559 N   0  0  0  0  0  2  0  0  0  0  0  0
   -0.8326    0.8604    0.5967 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2983    0.9090   -0.4543 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4660    0.1079    0.0418 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5882    0.0380   -0.7856 N   0  0  0  0  0  3  0  0  0  0  0  0
    3.4101    1.1440   -1.0585 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1417    0.8867    0.2394 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7271   -0.5509   -0.0645 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6788   -1.2668   -0.9164 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7080   -0.7167   -1.3746 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4510   -2.5900   -1.2351 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.7886    1.9223    0.3037 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9774    1.8294   -0.0150 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2969    3.2439    0.3938 O   0  0  0  0  0  1  0  0  0  0  0  0
   -2.5362   -2.2591   -0.7270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0322   -0.5880   -1.3167 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3782   -0.1050    1.2112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7287   -1.7117    1.5123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2963    1.2088    1.5388 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5064    1.9553   -0.6594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1497    0.4659   -1.3696 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0938   -0.9176    0.2573 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7244    0.5303    1.0594 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9976    2.1305   -1.2054 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1176    0.9101   -1.9082 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6278    1.2645    1.1279 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2292    1.0124    0.2099 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4042   -1.1302    0.8214 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
  9 19  1  0
 19 20  2  0
 19 21  1  0
 15 12  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
  9 26  1  0
 10 27  1  0
 10 28  1  0
 11 29  1  0
 11 30  1  0
 13 31  1  0
 13 32  1  0
 14 33  1  0
 14 34  1  0
 15 35  1  0
M  CHG  5   3  -1   8   1  12   1  18  -1  21  -1
M  RAD  2   8   3  12   2
M  END
Download

PDB for HMDB0304096 (3''-deamino-3''-oxonicotianamine)

HEADER    PROTEIN                                 14-MAY-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-15         0                                  
HETATM    1  C   UNK     0       3.564  -0.266   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.564  -1.806   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.230  -2.576   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.897  -1.806   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -0.437  -2.576   0.000  0.00  0.00           N+1
HETATM    6  C   UNK     0      -0.836  -4.064   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.323  -3.665   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.925  -2.178   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.066  -5.398   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.836  -6.731   0.000  0.00  0.00           O-1
HETATM   11  O   UNK     0       1.474  -5.398   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0       4.898  -2.576   0.000  0.00  0.00           N+1
HETATM   13  C   UNK     0       6.231  -1.806   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.565  -2.576   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.899  -1.806   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.232  -2.576   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      11.566  -1.806   0.000  0.00  0.00           O-1
HETATM   18  O   UNK     0      10.232  -4.116   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       8.899  -0.266   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       4.898   0.504   0.000  0.00  0.00           O-1
HETATM   21  O   UNK     0       2.230   0.504   0.000  0.00  0.00           O+0
CONECT    1    2   20   21                                                  
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    8                                                  
CONECT    6    5    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7    5                                                       
CONECT    9    6   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    2   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   19                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   15                                                            
CONECT   20    1                                                            
CONECT   21    1                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END
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3D PDB for HMDB0304096 (3''-deamino-3''-oxonicotianamine)

COMPND    HMDB0304096
HETATM    1  O1  UNL     1      -5.258   0.267  -1.413  1.00  0.00           O  
HETATM    2  C1  UNL     1      -5.570  -0.800  -0.827  1.00  0.00           C  
HETATM    3  O2  UNL     1      -6.925  -1.066  -0.685  1.00  0.00           O1-
HETATM    4  C2  UNL     1      -4.534  -1.679  -0.338  1.00  0.00           C  
HETATM    5  O3  UNL     1      -4.854  -2.737   0.241  1.00  0.00           O  
HETATM    6  C3  UNL     1      -3.113  -1.330  -0.522  1.00  0.00           C  
HETATM    7  C4  UNL     1      -2.617  -0.810   0.830  1.00  0.00           C  
HETATM    8  N1  UNL     1      -1.282  -0.429   0.856  1.00  0.00           N1+
HETATM    9  C5  UNL     1      -0.833   0.860   0.597  1.00  0.00           C  
HETATM   10  C6  UNL     1       0.298   0.909  -0.454  1.00  0.00           C  
HETATM   11  C7  UNL     1       1.466   0.108   0.042  1.00  0.00           C  
HETATM   12  N2  UNL     1       2.588   0.038  -0.786  1.00  0.00           N1+
HETATM   13  C8  UNL     1       3.410   1.144  -1.059  1.00  0.00           C  
HETATM   14  C9  UNL     1       4.142   0.887   0.239  1.00  0.00           C  
HETATM   15  C10 UNL     1       3.727  -0.551  -0.064  1.00  0.00           C  
HETATM   16  C11 UNL     1       4.679  -1.267  -0.916  1.00  0.00           C  
HETATM   17  O4  UNL     1       5.708  -0.717  -1.375  1.00  0.00           O  
HETATM   18  O5  UNL     1       4.451  -2.590  -1.235  1.00  0.00           O1-
HETATM   19  C12 UNL     1      -1.789   1.922   0.304  1.00  0.00           C  
HETATM   20  O6  UNL     1      -2.977   1.829  -0.015  1.00  0.00           O  
HETATM   21  O7  UNL     1      -1.297   3.244   0.394  1.00  0.00           O1-
HETATM   22  H1  UNL     1      -2.536  -2.259  -0.727  1.00  0.00           H  
HETATM   23  H2  UNL     1      -3.032  -0.588  -1.317  1.00  0.00           H  
HETATM   24  H3  UNL     1      -3.378  -0.105   1.211  1.00  0.00           H  
HETATM   25  H4  UNL     1      -2.729  -1.712   1.512  1.00  0.00           H  
HETATM   26  H5  UNL     1      -0.296   1.209   1.539  1.00  0.00           H  
HETATM   27  H6  UNL     1       0.506   1.955  -0.659  1.00  0.00           H  
HETATM   28  H7  UNL     1      -0.150   0.466  -1.370  1.00  0.00           H  
HETATM   29  H8  UNL     1       1.094  -0.918   0.257  1.00  0.00           H  
HETATM   30  H9  UNL     1       1.724   0.530   1.059  1.00  0.00           H  
HETATM   31  H10 UNL     1       2.998   2.130  -1.205  1.00  0.00           H  
HETATM   32  H11 UNL     1       4.118   0.910  -1.908  1.00  0.00           H  
HETATM   33  H12 UNL     1       3.628   1.264   1.128  1.00  0.00           H  
HETATM   34  H13 UNL     1       5.229   1.012   0.210  1.00  0.00           H  
HETATM   35  H14 UNL     1       3.404  -1.130   0.821  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    4    5    5    6
CONECT    6    7   22   23
CONECT    7    8   24   25
CONECT    8    9
CONECT    9   10   19   26
CONECT   10   11   27   28
CONECT   11   12   29   30
CONECT   12   13   15
CONECT   13   14   31   32
CONECT   14   15   33   34
CONECT   15   16   35
CONECT   16   17   17   18
CONECT   19   20   20   21
END
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SMILES for HMDB0304096 (3''-deamino-3''-oxonicotianamine)

[O-]C(=O)C(CC[N+]1CCC1C([O-])=O)[N+]CCC(=O)C([O-])=O
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INCHI for HMDB0304096 (3''-deamino-3''-oxonicotianamine)

InChI=1S/C12H17N2O7/c15-9(12(20)21)1-4-13-7(10(16)17)2-5-14-6-3-8(14)11(18)19/h7-8H,1-6H2,(H,16,17)(H,18,19)(H,20,21)/q+2/p-3
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC12H14N2O7
Average Molecular Weight298.252
Monoisotopic Molecular Weight298.080649379
IUPAC Name2-carboxylato-1-{3-carboxylato-3-[(3-carboxylato-3-oxopropyl)azaniumyl]propyl}azetidin-1-ium-1-yl
Traditional Name2-carboxylato-1-{3-carboxylato-3-[(3-carboxylato-3-oxopropyl)ammonio]propyl}azetidin-1-ium-1-yl
CAS Registry NumberNot Available
SMILES
[O-]C(=O)C(CC[N+]1CCC1C([O-])=O)[N+]CCC(=O)C([O-])=O
InChI Identifier
InChI=1S/C12H17N2O7/c15-9(12(20)21)1-4-13-7(10(16)17)2-5-14-6-3-8(14)11(18)19/h7-8H,1-6H2,(H,16,17)(H,18,19)(H,20,21)/q+2/p-3
InChI KeyRPGJYKVCHUARBL-UHFFFAOYSA-K
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids
Alternative Parents
Substituents
  • Alpha-amino acid
  • Tricarboxylic acid or derivatives
  • Azetidinecarboxylic acid
  • Keto acid
  • Alpha-keto acid
  • Ketone
  • Carboxylic acid salt
  • Azetidine
  • Azacycle
  • Organoheterocyclic compound
  • Carboxylic acid
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organic salt
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Organic anion
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP0.82ALOGPS
logP-2.3ChemAxon
logS-4.1ALOGPS
pKa (Strongest Acidic)1.76ChemAxon
pKa (Strongest Basic)-9.8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area160.28 ŲChemAxon
Rotatable Bond Count10ChemAxon
Refractivity100.18 m³·mol⁻¹ChemAxon
Polarizability27.45 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+155.31632859911
AllCCS[M+H-H2O]+152.49432859911
AllCCS[M+Na]+158.67132859911
AllCCS[M+NH4]+157.92332859911
AllCCS[M-H]-149.69932859911
AllCCS[M+Na-2H]-147.99632859911
AllCCS[M+HCOO]-146.25332859911
DeepCCS[M+H]+161.54530932474
DeepCCS[M-H]-159.16230932474
DeepCCS[M-2H]-192.04730932474
DeepCCS[M+Na]+167.61330932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3''-deamino-3''-oxonicotianamine,1TMS,isomer #1C[Si](C)(C)OC(=CC[N+]C(CC[N+]1CCC1C(=O)[O-])C(=O)[O-])C(=O)[O-]2313.9Semi standard non polar33892256
3''-deamino-3''-oxonicotianamine,1TMS,isomer #1C[Si](C)(C)OC(=CC[N+]C(CC[N+]1CCC1C(=O)[O-])C(=O)[O-])C(=O)[O-]2358.7Standard non polar33892256
3''-deamino-3''-oxonicotianamine,1TMS,isomer #1C[Si](C)(C)OC(=CC[N+]C(CC[N+]1CCC1C(=O)[O-])C(=O)[O-])C(=O)[O-]3364.4Standard polar33892256
3''-deamino-3''-oxonicotianamine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=CC[N+]C(CC[N+]1CCC1C(=O)[O-])C(=O)[O-])C(=O)[O-]2559.7Semi standard non polar33892256
3''-deamino-3''-oxonicotianamine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=CC[N+]C(CC[N+]1CCC1C(=O)[O-])C(=O)[O-])C(=O)[O-]2587.0Standard non polar33892256
3''-deamino-3''-oxonicotianamine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=CC[N+]C(CC[N+]1CCC1C(=O)[O-])C(=O)[O-])C(=O)[O-]3394.8Standard polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3''-deamino-3''-oxonicotianamine 10V, Negative-QTOFsplash10-0540-3090000000-bd5ab2174f66342934c82019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3''-deamino-3''-oxonicotianamine 20V, Negative-QTOFsplash10-0a4i-5290000000-b7dc3cbd9d59fbe2ea172019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3''-deamino-3''-oxonicotianamine 40V, Negative-QTOFsplash10-0kor-8970000000-95ae04398433e17ac5c92019-02-23Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030375
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available