MiMeDB: Showing metabocard for 3-oxosphinganine (MMDBc0054235)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:00:58 UTC

Update Date

2022-09-01 02:27:58 UTC

Metabolite ID

MMDBc0054235

Metabolite Identification

Common Name

3-oxosphinganine

Description

3-dehydrosphinganinium(1+), also known as 3-oxosphinganine, belongs to the class of organic compounds known as beta-hydroxy ketones. These are ketones containing a hydroxyl group attached to the beta-carbon atom, relative to the C=O group. 3-dehydrosphinganinium(1+) is a very strong basic compound (based on its pKa). A cationic sphingoid that is the conjugate acid of 3-dehydrosphinganine; major species at pH 7.3.

Structure

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

HMDB0062571
     RDKit          3D
3-dehydrosphinganinium(1+)
 59 58  0  0  0  0  0  0  0  0999 V2000
   -6.4711   -1.6172   -0.5395 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0632   -0.4432    0.3259 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1703    0.8615   -0.4047 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7489    2.0732    0.2789 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3533    2.4465    0.5026 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3219    1.5913    1.0578 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7309    0.5062    0.1995 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7387   -0.2310    1.0852 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0569   -1.3543    0.3689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2766   -0.8997   -0.8385 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8017    0.0783   -0.5049 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8342   -0.4453    0.4514 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5492   -1.6673   -0.0993 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5643   -2.1723    0.8705 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6219   -1.1881    1.2261 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4274   -0.7877    0.0752 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1915   -1.3043   -1.0065 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5396    0.2218    0.1216 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.1336    0.2452   -1.2137 N   0  0  0  0  0  4  0  0  0  0  0  0
    5.9411    1.5718    0.4124 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4000    1.5839    1.6793 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9475   -1.5223   -1.5172 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5693   -1.5606   -0.6872 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2183   -2.5519   -0.0160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1799   -0.5959    0.8814 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9008   -0.4294    1.1427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2486    0.9548   -0.7183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5967    0.8004   -1.3838 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3134    2.9394   -0.2401 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3321    2.1125    1.2995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9499    3.0326   -0.4176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4127    3.3567    1.2361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7752    1.0322    1.9429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4770    2.1497    1.5470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4030   -0.1344   -0.3327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1243    1.0068   -0.6533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3223   -0.6697    1.9193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0201    0.4795    1.5177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7996   -2.0822    0.0264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3900   -1.8550    1.0960 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9676   -0.4760   -1.5828 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1685   -1.8009   -1.3052 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4312    1.0496   -0.1710 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3520    0.2811   -1.4708 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6202    0.3624    0.5246 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4730   -0.6205    1.4694 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9898   -1.4678   -1.0766 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7909   -2.4921   -0.2964 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0154   -2.5383    1.7843 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0676   -3.0705    0.4382 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1362   -0.2795    1.6851 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2635   -1.6253    2.0320 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2726   -0.0698    0.8987 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4299    1.2239   -1.4645 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9137   -0.4304   -1.2225 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4180   -0.0321   -1.9161 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1092    1.7492   -0.3071 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6859    2.3910    0.2637 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7381    2.3133    1.7258 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  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
 18 19  1  0
 18 20  1  0
 20 21  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  2 26  1  0
  3 27  1  0
  3 28  1  0
  4 29  1  0
  4 30  1  0
  5 31  1  0
  5 32  1  0
  6 33  1  0
  6 34  1  0
  7 35  1  0
  7 36  1  0
  8 37  1  0
  8 38  1  0
  9 39  1  0
  9 40  1  0
 10 41  1  0
 10 42  1  0
 11 43  1  0
 11 44  1  0
 12 45  1  0
 12 46  1  0
 13 47  1  0
 13 48  1  0
 14 49  1  0
 14 50  1  0
 15 51  1  0
 15 52  1  0
 18 53  1  1
 19 54  1  0
 19 55  1  0
 19 56  1  0
 20 57  1  0
 20 58  1  0
 21 59  1  0
M  CHG  1  19   1
M  END


  Mrv1652303231705272D          

 22 21  0  0  1  0            999 V2000
    9.9000    6.5408    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.6145    6.1283    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.6145    6.9533    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    9.9000    5.7158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1855    6.1283    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.3289    5.7158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3289    4.8908    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0434    6.1283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7579    5.7158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4724    6.1283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.1868    5.7158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9013    6.1283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6158    5.7158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3302    6.1283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0447    5.7158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7592    6.1283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.4737    5.7158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.1881    6.1283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.9026    5.7158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.6171    6.1283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.3315    5.7158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.0460    6.1283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  6  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  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  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
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
M  CHG  1   3   1
M  END
> <DATABASE_ID>
MMDBc0054235

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]([NH3+])(CO)C(=O)CCCCCCCCCCCCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C18H37NO2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-18(21)17(19)16-20/h17,20H,2-16,19H2,1H3/p+1/t17-/m0/s1

> <INCHI_KEY>
KBUNOSOGGAARKZ-KRWDZBQOSA-O

> <FORMULA>
C18H38NO2

> <MOLECULAR_WEIGHT>
300.506

> <EXACT_MASS>
300.289705888

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
59

> <JCHEM_AVERAGE_POLARIZABILITY>
39.91661509421692

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S)-1-hydroxy-3-oxooctadecan-2-aminium

> <ALOGPS_LOGP>
3.27

> <JCHEM_LOGP>
5.183932733333332

> <ALOGPS_LOGS>
-6.38

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
15.776671018108978

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.375515999596963

> <JCHEM_PKA_STRONGEST_BASIC>
7.535784702603497

> <JCHEM_POLAR_SURFACE_AREA>
64.94

> <JCHEM_REFRACTIVITY>
101.3248

> <JCHEM_ROTATABLE_BOND_COUNT>
16

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.39e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-dehydro-D-sphinganine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0062571
     RDKit          3D
3-dehydrosphinganinium(1+)
 59 58  0  0  0  0  0  0  0  0999 V2000
   -6.4711   -1.6172   -0.5395 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0632   -0.4432    0.3259 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1703    0.8615   -0.4047 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7489    2.0732    0.2789 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3533    2.4465    0.5026 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3219    1.5913    1.0578 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7309    0.5062    0.1995 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7387   -0.2310    1.0852 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0569   -1.3543    0.3689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2766   -0.8997   -0.8385 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8017    0.0783   -0.5049 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8342   -0.4453    0.4514 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5492   -1.6673   -0.0993 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5643   -2.1723    0.8705 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6219   -1.1881    1.2261 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4274   -0.7877    0.0752 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1915   -1.3043   -1.0065 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5396    0.2218    0.1216 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.1336    0.2452   -1.2137 N   0  0  0  0  0  4  0  0  0  0  0  0
    5.9411    1.5718    0.4124 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4000    1.5839    1.6793 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9475   -1.5223   -1.5172 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5693   -1.5606   -0.6872 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2183   -2.5519   -0.0160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1799   -0.5959    0.8814 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9008   -0.4294    1.1427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2486    0.9548   -0.7183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5967    0.8004   -1.3838 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3134    2.9394   -0.2401 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3321    2.1125    1.2995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9499    3.0326   -0.4176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4127    3.3567    1.2361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7752    1.0322    1.9429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4770    2.1497    1.5470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4030   -0.1344   -0.3327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1243    1.0068   -0.6533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3223   -0.6697    1.9193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0201    0.4795    1.5177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7996   -2.0822    0.0264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3900   -1.8550    1.0960 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9676   -0.4760   -1.5828 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1685   -1.8009   -1.3052 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4312    1.0496   -0.1710 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3520    0.2811   -1.4708 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6202    0.3624    0.5246 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4730   -0.6205    1.4694 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9898   -1.4678   -1.0766 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7909   -2.4921   -0.2964 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0154   -2.5383    1.7843 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0676   -3.0705    0.4382 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1362   -0.2795    1.6851 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2635   -1.6253    2.0320 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2726   -0.0698    0.8987 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4299    1.2239   -1.4645 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9137   -0.4304   -1.2225 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4180   -0.0321   -1.9161 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1092    1.7492   -0.3071 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6859    2.3910    0.2637 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7381    2.3133    1.7258 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  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
 18 19  1  0
 18 20  1  0
 20 21  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  2 26  1  0
  3 27  1  0
  3 28  1  0
  4 29  1  0
  4 30  1  0
  5 31  1  0
  5 32  1  0
  6 33  1  0
  6 34  1  0
  7 35  1  0
  7 36  1  0
  8 37  1  0
  8 38  1  0
  9 39  1  0
  9 40  1  0
 10 41  1  0
 10 42  1  0
 11 43  1  0
 11 44  1  0
 12 45  1  0
 12 46  1  0
 13 47  1  0
 13 48  1  0
 14 49  1  0
 14 50  1  0
 15 51  1  0
 15 52  1  0
 18 53  1  1
 19 54  1  0
 19 55  1  0
 19 56  1  0
 20 57  1  0
 20 58  1  0
 21 59  1  0
M  CHG  1  19   1
M  END

HEADER    PROTEIN                                 23-MAR-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-MAR-17         0                                  
HETATM    1  H   UNK     0      18.480  12.209   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0      19.814  11.439   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      19.814  12.979   0.000  0.00  0.00           N+1
HETATM    4  C   UNK     0      18.480  10.669   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      17.146  11.439   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      21.147  10.669   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      21.147   9.129   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      22.481  11.439   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      23.815  10.669   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      25.148  11.439   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      26.482  10.669   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      27.816  11.439   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      29.149  10.669   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      30.483  11.439   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      31.817  10.669   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      33.150  11.439   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      34.484  10.669   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      35.818  11.439   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      37.152  10.669   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      38.485  11.439   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      39.819  10.669   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      41.153  11.439   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4    6                                             
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4                                                            
CONECT    6    2    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   42    0
END

COMPND    HMDB0062571
HETATM    1  C1  UNL     1      -6.471  -1.617  -0.540  1.00  0.00           C  
HETATM    2  C2  UNL     1      -6.063  -0.443   0.326  1.00  0.00           C  
HETATM    3  C3  UNL     1      -6.170   0.861  -0.405  1.00  0.00           C  
HETATM    4  C4  UNL     1      -5.749   2.073   0.279  1.00  0.00           C  
HETATM    5  C5  UNL     1      -4.353   2.446   0.503  1.00  0.00           C  
HETATM    6  C6  UNL     1      -3.322   1.591   1.058  1.00  0.00           C  
HETATM    7  C7  UNL     1      -2.731   0.506   0.199  1.00  0.00           C  
HETATM    8  C8  UNL     1      -1.739  -0.231   1.085  1.00  0.00           C  
HETATM    9  C9  UNL     1      -1.057  -1.354   0.369  1.00  0.00           C  
HETATM   10  C10 UNL     1      -0.277  -0.900  -0.839  1.00  0.00           C  
HETATM   11  C11 UNL     1       0.802   0.078  -0.505  1.00  0.00           C  
HETATM   12  C12 UNL     1       1.834  -0.445   0.451  1.00  0.00           C  
HETATM   13  C13 UNL     1       2.549  -1.667  -0.099  1.00  0.00           C  
HETATM   14  C14 UNL     1       3.564  -2.172   0.870  1.00  0.00           C  
HETATM   15  C15 UNL     1       4.622  -1.188   1.226  1.00  0.00           C  
HETATM   16  C16 UNL     1       5.427  -0.788   0.075  1.00  0.00           C  
HETATM   17  O1  UNL     1       5.192  -1.304  -1.007  1.00  0.00           O  
HETATM   18  C17 UNL     1       6.540   0.222   0.122  1.00  0.00           C  
HETATM   19  N1  UNL     1       7.134   0.245  -1.214  1.00  0.00           N1+
HETATM   20  C18 UNL     1       5.941   1.572   0.412  1.00  0.00           C  
HETATM   21  O2  UNL     1       5.400   1.584   1.679  1.00  0.00           O  
HETATM   22  H1  UNL     1      -5.948  -1.522  -1.517  1.00  0.00           H  
HETATM   23  H2  UNL     1      -7.569  -1.561  -0.687  1.00  0.00           H  
HETATM   24  H3  UNL     1      -6.218  -2.552  -0.016  1.00  0.00           H  
HETATM   25  H4  UNL     1      -5.180  -0.596   0.881  1.00  0.00           H  
HETATM   26  H5  UNL     1      -6.901  -0.429   1.143  1.00  0.00           H  
HETATM   27  H6  UNL     1      -7.249   0.955  -0.718  1.00  0.00           H  
HETATM   28  H7  UNL     1      -5.597   0.800  -1.384  1.00  0.00           H  
HETATM   29  H8  UNL     1      -6.313   2.939  -0.240  1.00  0.00           H  
HETATM   30  H9  UNL     1      -6.332   2.113   1.299  1.00  0.00           H  
HETATM   31  H10 UNL     1      -3.950   3.033  -0.418  1.00  0.00           H  
HETATM   32  H11 UNL     1      -4.413   3.357   1.236  1.00  0.00           H  
HETATM   33  H12 UNL     1      -3.775   1.032   1.943  1.00  0.00           H  
HETATM   34  H13 UNL     1      -2.477   2.150   1.547  1.00  0.00           H  
HETATM   35  H14 UNL     1      -3.403  -0.134  -0.333  1.00  0.00           H  
HETATM   36  H15 UNL     1      -2.124   1.007  -0.653  1.00  0.00           H  
HETATM   37  H16 UNL     1      -2.322  -0.670   1.919  1.00  0.00           H  
HETATM   38  H17 UNL     1      -1.020   0.479   1.518  1.00  0.00           H  
HETATM   39  H18 UNL     1      -1.800  -2.082   0.026  1.00  0.00           H  
HETATM   40  H19 UNL     1      -0.390  -1.855   1.096  1.00  0.00           H  
HETATM   41  H20 UNL     1      -0.968  -0.476  -1.583  1.00  0.00           H  
HETATM   42  H21 UNL     1       0.169  -1.801  -1.305  1.00  0.00           H  
HETATM   43  H22 UNL     1       0.431   1.050  -0.171  1.00  0.00           H  
HETATM   44  H23 UNL     1       1.352   0.281  -1.471  1.00  0.00           H  
HETATM   45  H24 UNL     1       2.620   0.362   0.525  1.00  0.00           H  
HETATM   46  H25 UNL     1       1.473  -0.621   1.469  1.00  0.00           H  
HETATM   47  H26 UNL     1       2.990  -1.468  -1.077  1.00  0.00           H  
HETATM   48  H27 UNL     1       1.791  -2.492  -0.296  1.00  0.00           H  
HETATM   49  H28 UNL     1       3.015  -2.538   1.784  1.00  0.00           H  
HETATM   50  H29 UNL     1       4.068  -3.071   0.438  1.00  0.00           H  
HETATM   51  H30 UNL     1       4.136  -0.280   1.685  1.00  0.00           H  
HETATM   52  H31 UNL     1       5.263  -1.625   2.032  1.00  0.00           H  
HETATM   53  H32 UNL     1       7.273  -0.070   0.899  1.00  0.00           H  
HETATM   54  H33 UNL     1       7.430   1.224  -1.465  1.00  0.00           H  
HETATM   55  H34 UNL     1       7.914  -0.430  -1.222  1.00  0.00           H  
HETATM   56  H35 UNL     1       6.418  -0.032  -1.916  1.00  0.00           H  
HETATM   57  H36 UNL     1       5.109   1.749  -0.307  1.00  0.00           H  
HETATM   58  H37 UNL     1       6.686   2.391   0.264  1.00  0.00           H  
HETATM   59  H38 UNL     1       4.738   2.313   1.726  1.00  0.00           H  
CONECT    1    2   22   23   24
CONECT    2    3   25   26
CONECT    3    4   27   28
CONECT    4    5   29   30
CONECT    5    6   31   32
CONECT    6    7   33   34
CONECT    7    8   35   36
CONECT    8    9   37   38
CONECT    9   10   39   40
CONECT   10   11   41   42
CONECT   11   12   43   44
CONECT   12   13   45   46
CONECT   13   14   47   48
CONECT   14   15   49   50
CONECT   15   16   51   52
CONECT   16   17   17   18
CONECT   18   19   20   53
CONECT   19   54   55   56
CONECT   20   21   57   58
CONECT   21   59
END

HMDB0062571
     RDKit          3D
3-dehydrosphinganinium(1+)
 59 58  0  0  0  0  0  0  0  0999 V2000
   -6.4711   -1.6172   -0.5395 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0632   -0.4432    0.3259 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1703    0.8615   -0.4047 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7489    2.0732    0.2789 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3533    2.4465    0.5026 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3219    1.5913    1.0578 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7309    0.5062    0.1995 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7387   -0.2310    1.0852 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0569   -1.3543    0.3689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2766   -0.8997   -0.8385 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8017    0.0783   -0.5049 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8342   -0.4453    0.4514 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5492   -1.6673   -0.0993 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5643   -2.1723    0.8705 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6219   -1.1881    1.2261 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4274   -0.7877    0.0752 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1915   -1.3043   -1.0065 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5396    0.2218    0.1216 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.1336    0.2452   -1.2137 N   0  0  0  0  0  4  0  0  0  0  0  0
    5.9411    1.5718    0.4124 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4000    1.5839    1.6793 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9475   -1.5223   -1.5172 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5693   -1.5606   -0.6872 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2183   -2.5519   -0.0160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1799   -0.5959    0.8814 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9008   -0.4294    1.1427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2486    0.9548   -0.7183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5967    0.8004   -1.3838 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3134    2.9394   -0.2401 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3321    2.1125    1.2995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9499    3.0326   -0.4176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4127    3.3567    1.2361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7752    1.0322    1.9429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4770    2.1497    1.5470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4030   -0.1344   -0.3327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1243    1.0068   -0.6533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3223   -0.6697    1.9193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0201    0.4795    1.5177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7996   -2.0822    0.0264 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3900   -1.8550    1.0960 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9676   -0.4760   -1.5828 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1685   -1.8009   -1.3052 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4312    1.0496   -0.1710 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3520    0.2811   -1.4708 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6202    0.3624    0.5246 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4730   -0.6205    1.4694 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9898   -1.4678   -1.0766 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7909   -2.4921   -0.2964 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0154   -2.5383    1.7843 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0676   -3.0705    0.4382 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1362   -0.2795    1.6851 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2635   -1.6253    2.0320 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2726   -0.0698    0.8987 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4299    1.2239   -1.4645 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9137   -0.4304   -1.2225 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4180   -0.0321   -1.9161 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1092    1.7492   -0.3071 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6859    2.3910    0.2637 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7381    2.3133    1.7258 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  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
 18 19  1  0
 18 20  1  0
 20 21  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  2 26  1  0
  3 27  1  0
  3 28  1  0
  4 29  1  0
  4 30  1  0
  5 31  1  0
  5 32  1  0
  6 33  1  0
  6 34  1  0
  7 35  1  0
  7 36  1  0
  8 37  1  0
  8 38  1  0
  9 39  1  0
  9 40  1  0
 10 41  1  0
 10 42  1  0
 11 43  1  0
 11 44  1  0
 12 45  1  0
 12 46  1  0
 13 47  1  0
 13 48  1  0
 14 49  1  0
 14 50  1  0
 15 51  1  0
 15 52  1  0
 18 53  1  1
 19 54  1  0
 19 55  1  0
 19 56  1  0
 20 57  1  0
 20 58  1  0
 21 59  1  0
M  CHG  1  19   1
M  END

Synonyms

Value	Source
3-Dehydrosphinganinium	ChEBI
3-Dehydrosphinganinium cation	ChEBI
3-Oxosphinganine	ChEBI

Molecular Formula

C₁₈H₃₈NO₂

Average Mass

300.506

Monoisotopic Mass

300.289705888

IUPAC Name

(2S)-1-hydroxy-3-oxooctadecan-2-aminium

Traditional Name

3-dehydro-D-sphinganine

CAS Registry Number

Not Available

SMILES

[H][C@]([NH3+])(CO)C(=O)CCCCCCCCCCCCCCC

InChI Identifier

InChI=1S/C18H37NO2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-18(21)17(19)16-20/h17,20H,2-16,19H2,1H3/p+1/t17-/m0/s1

InChI Key

KBUNOSOGGAARKZ-KRWDZBQOSA-O

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta-hydroxy ketones. These are ketones containing a hydroxyl group attached to the beta-carbon atom, relative to the C=O group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Beta-hydroxy ketones

Alternative Parents

Substituents

Beta-hydroxy ketone
Alpha-aminoketone
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Primary alcohol
Organonitrogen compound
Primary aliphatic amine
Amine
Alcohol
Organic cation
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

3-dehydrosphingoid base(1+) (CHEBI:58299 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.00014 g/L	ALOGPS
logP	3.27	ALOGPS
logP	5.18	ChemAxon
logS	-6.4	ALOGPS
pKa (Strongest Acidic)	14.38	ChemAxon
pKa (Strongest Basic)	7.54	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	64.94 Å²	ChemAxon
Rotatable Bond Count	16	ChemAxon
Refractivity	101.32 m³·mol⁻¹	ChemAxon
Polarizability	39.92 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-06s9-9230000000-7a053911f92a509f920c	2017-09-20	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-001i-2901000000-c447c2bd7e85a065386d	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0w30-5196000000-5908fe1b0544e33c707e	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03e9-7491000000-f4d60e936262e5ff65f8	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03dl-9200000000-5dd70d2e638c4fe4dd3c	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0f89-1091000000-4489cb628395794fee25	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0ue9-2190000000-32fec42fec706ce6576c	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4l-9100000000-b071fe68f1e76058e33f	2021-09-25	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0014232	NADP(+)	3-oxosphinganine	3-ketodihydrosphingosine reductase TSC10	Reduction	RHEA	34755880
MMDBr0017865	Hydrogen Ion	3-oxosphinganine	Serine palmitoyltransferase 1	Transfer of a palmitoyl group	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	10
Eukaryota/Fungi	Basidiomycota	2

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

HMDB0062571

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

49852310

PDB ID

Not Available

ChEBI ID

58299

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for 3-oxosphinganine (MMDBc0054235)

MOL for #<Metabolite:0x00007fa4e0c01070>

3D MOL for #<Metabolite:0x00007fa4e0c01070>

3D SDF for #<Metabolite:0x00007fa4e0c01070>

3D-SDF for #<Metabolite:0x00007fa4e0c01070>

PDB for #<Metabolite:0x00007fa4e0c01070>

3D PDB for #<Metabolite:0x00007fa4e0c01070>

SMILES for #<Metabolite:0x00007fa4e0c01070>

INCHI for #<Metabolite:0x00007fa4e0c01070>

Structure for #<Metabolite:0x00007fa4e0c01070>

3D Structure for #<Metabolite:0x00007fa4e0c01070>