MiMeDB: Showing metabocard for (S)-Succinyldihydrolipoamide (MMDBc0031895)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:53:52 UTC

Update Date

2022-08-31 18:25:49 UTC

Metabolite ID

MMDBc0031895

Metabolite Identification

Common Name

(S)-Succinyldihydrolipoamide

Description

(S)-Succinyldihydrolipoamide is a metabolite (a product as well as a substrate) in glutamate degradation. It is also invovled in citrate cycle and is a reactant for oxoglutarate dehydrogenase (EC 1.2.4.2) and dihydrolipoyllysine-residue succinyltransferase (EC 2.3.1.61).

Structure

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

HMDB0001177
     RDKit          3D
(S)-Succinyldihydrolipoamide
 40 39  0  0  0  0  0  0  0  0999 V2000
    6.0119   -2.2906   -0.2168 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7416   -2.1043    0.3712 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3245   -2.8707    1.2636 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9058   -0.9789   -0.0893 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6008   -1.0130    0.6625 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7297    0.1434    0.1937 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4261    0.0472    0.9840 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4854    1.1459    0.5672 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1493    2.5159    0.8388 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8155    3.6155    0.4088 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0922    5.2387    0.7172 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0997    1.1601    1.3061 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1439   -0.1125    0.7196 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2803   -0.2738    1.2055 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7479   -1.0377   -0.3550 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9081   -1.9552   -0.7543 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0080   -1.1186   -1.2274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9549    0.1323   -1.2920 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2093   -1.7048   -1.6428 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5264   -3.1808   -0.0394 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4475   -1.5798   -0.8139 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7691   -1.0169   -1.1771 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4297   -0.0432    0.2301 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0578   -1.9501    0.4824 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7494   -0.8949    1.7535 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2779    1.0743    0.3710 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5122    0.0178   -0.8720 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6754    0.1341    2.0743 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0426   -0.9470    0.8163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5580    1.1264   -0.5658 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3947    2.6341    1.8912 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0430    2.6178    0.2106 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0164    3.5050   -0.6803 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7579    3.5436    0.9804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4744    6.1594   -0.2779 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9368   -1.6926    0.0004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3908   -0.4634   -1.2318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2348   -2.5727    0.0851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5644   -2.6393   -1.5635 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1368   -2.3704   -2.4058 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  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
  8 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 17 19  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  4 23  1  0
  5 24  1  0
  5 25  1  0
  6 26  1  0
  6 27  1  0
  7 28  1  0
  7 29  1  0
  8 30  1  6
  9 31  1  0
  9 32  1  0
 10 33  1  0
 10 34  1  0
 11 35  1  0
 15 36  1  0
 15 37  1  0
 16 38  1  0
 16 39  1  0
 19 40  1  0
M  END


  Mrv0541 02231218582D          

 19 18  0  0  1  0            999 V2000
   -1.2341   -0.8491    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2376   -0.0206    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5191   -1.2582    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9492   -1.2651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5294    0.3885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1960   -0.8457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6608   -0.8526    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5328    1.2134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1856   -0.0206    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9075   -1.2547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6641   -0.0275    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.1787    1.6260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6226   -0.8388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1754    2.4510    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3376   -1.2513    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8835    2.8601    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5431    2.8601    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0491   -0.8353    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3342   -2.0764    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  6  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  4  7  1  0  0  0  0
  5  8  1  0  0  0  0
  5  9  2  0  0  0  0
  6 10  1  0  0  0  0
  7 11  1  0  0  0  0
  8 12  1  0  0  0  0
 10 13  1  0  0  0  0
 12 14  1  0  0  0  0
 13 15  1  0  0  0  0
 14 16  1  0  0  0  0
 14 17  2  0  0  0  0
 15 18  1  0  0  0  0
 15 19  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031895

> <DATABASE_NAME>
MIME

> <SMILES>
NC(=O)CCCC[C@H](CCS)SC(=O)CCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C12H21NO4S2/c13-10(14)4-2-1-3-9(7-8-18)19-12(17)6-5-11(15)16/h9,18H,1-8H2,(H2,13,14)(H,15,16)/t9-/m1/s1

> <INCHI_KEY>
RJCJWONCSKSHES-SECBINFHSA-N

> <FORMULA>
C12H21NO4S2

> <MOLECULAR_WEIGHT>
307.429

> <EXACT_MASS>
307.091199545

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
32.861049423013746

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-{[(3R)-7-carbamoyl-1-sulfanylheptan-3-yl]sulfanyl}-4-oxobutanoic acid

> <ALOGPS_LOGP>
1.97

> <JCHEM_LOGP>
1.061330826

> <ALOGPS_LOGS>
-3.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
10.190901926454105

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.376388081756565

> <JCHEM_PKA_STRONGEST_BASIC>
-0.5791148779299317

> <JCHEM_POLAR_SURFACE_AREA>
97.46000000000001

> <JCHEM_REFRACTIVITY>
78.11989999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.05e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-{[(3R)-7-carbamoyl-1-sulfanylheptan-3-yl]sulfanyl}-4-oxobutanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0001177
     RDKit          3D
(S)-Succinyldihydrolipoamide
 40 39  0  0  0  0  0  0  0  0999 V2000
    6.0119   -2.2906   -0.2168 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7416   -2.1043    0.3712 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3245   -2.8707    1.2636 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9058   -0.9789   -0.0893 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6008   -1.0130    0.6625 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7297    0.1434    0.1937 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4261    0.0472    0.9840 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4854    1.1459    0.5672 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1493    2.5159    0.8388 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8155    3.6155    0.4088 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0922    5.2387    0.7172 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0997    1.1601    1.3061 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1439   -0.1125    0.7196 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2803   -0.2738    1.2055 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7479   -1.0377   -0.3550 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9081   -1.9552   -0.7543 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0080   -1.1186   -1.2274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9549    0.1323   -1.2920 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2093   -1.7048   -1.6428 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5264   -3.1808   -0.0394 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4475   -1.5798   -0.8139 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7691   -1.0169   -1.1771 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4297   -0.0432    0.2301 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0578   -1.9501    0.4824 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7494   -0.8949    1.7535 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2779    1.0743    0.3710 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5122    0.0178   -0.8720 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6754    0.1341    2.0743 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0426   -0.9470    0.8163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5580    1.1264   -0.5658 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3947    2.6341    1.8912 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0430    2.6178    0.2106 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0164    3.5050   -0.6803 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7579    3.5436    0.9804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4744    6.1594   -0.2779 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9368   -1.6926    0.0004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3908   -0.4634   -1.2318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2348   -2.5727    0.0851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5644   -2.6393   -1.5635 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1368   -2.3704   -2.4058 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  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
  8 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 17 19  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  4 23  1  0
  5 24  1  0
  5 25  1  0
  6 26  1  0
  6 27  1  0
  7 28  1  0
  7 29  1  0
  8 30  1  6
  9 31  1  0
  9 32  1  0
 10 33  1  0
 10 34  1  0
 11 35  1  0
 15 36  1  0
 15 37  1  0
 16 38  1  0
 16 39  1  0
 19 40  1  0
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      -2.304  -1.585   0.000  0.00  0.00           C+0
HETATM    2  S   UNK     0      -2.310  -0.038   0.000  0.00  0.00           S+0
HETATM    3  C   UNK     0      -0.969  -2.349   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.639  -2.362   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.988   0.725   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.366  -1.579   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -4.967  -1.592   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.995   2.265   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       0.346  -0.038   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       1.694  -2.342   0.000  0.00  0.00           C+0
HETATM   11  S   UNK     0      -4.973  -0.051   0.000  0.00  0.00           S+0
HETATM   12  C   UNK     0       0.334   3.035   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.029  -1.566   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.327   4.575   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.364  -2.336   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       1.649   5.339   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -1.014   5.339   0.000  0.00  0.00           O+0
HETATM   18  N   UNK     0       5.692  -1.559   0.000  0.00  0.00           N+0
HETATM   19  O   UNK     0       4.357  -3.876   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5                                                       
CONECT    3    1    6                                                       
CONECT    4    1    7                                                       
CONECT    5    2    8    9                                                  
CONECT    6    3   10                                                       
CONECT    7    4   11                                                       
CONECT    8    5   12                                                       
CONECT    9    5                                                            
CONECT   10    6   13                                                       
CONECT   11    7                                                            
CONECT   12    8   14                                                       
CONECT   13   10   15                                                       
CONECT   14   12   16   17                                                  
CONECT   15   13   18   19                                                  
CONECT   16   14                                                            
CONECT   17   14                                                            
CONECT   18   15                                                            
CONECT   19   15                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   36    0
END

COMPND    HMDB0001177
HETATM    1  N1  UNL     1       6.012  -2.291  -0.217  1.00  0.00           N  
HETATM    2  C1  UNL     1       4.742  -2.104   0.371  1.00  0.00           C  
HETATM    3  O1  UNL     1       4.325  -2.871   1.264  1.00  0.00           O  
HETATM    4  C2  UNL     1       3.906  -0.979  -0.089  1.00  0.00           C  
HETATM    5  C3  UNL     1       2.601  -1.013   0.662  1.00  0.00           C  
HETATM    6  C4  UNL     1       1.730   0.143   0.194  1.00  0.00           C  
HETATM    7  C5  UNL     1       0.426   0.047   0.984  1.00  0.00           C  
HETATM    8  C6  UNL     1      -0.485   1.146   0.567  1.00  0.00           C  
HETATM    9  C7  UNL     1       0.149   2.516   0.839  1.00  0.00           C  
HETATM   10  C8  UNL     1      -0.815   3.615   0.409  1.00  0.00           C  
HETATM   11  S1  UNL     1      -0.092   5.239   0.717  1.00  0.00           S  
HETATM   12  S2  UNL     1      -2.100   1.160   1.306  1.00  0.00           S  
HETATM   13  C9  UNL     1      -3.144  -0.113   0.720  1.00  0.00           C  
HETATM   14  O2  UNL     1      -4.280  -0.274   1.205  1.00  0.00           O  
HETATM   15  C10 UNL     1      -2.748  -1.038  -0.355  1.00  0.00           C  
HETATM   16  C11 UNL     1      -3.908  -1.955  -0.754  1.00  0.00           C  
HETATM   17  C12 UNL     1      -5.008  -1.119  -1.227  1.00  0.00           C  
HETATM   18  O3  UNL     1      -4.955   0.132  -1.292  1.00  0.00           O  
HETATM   19  O4  UNL     1      -6.209  -1.705  -1.643  1.00  0.00           O  
HETATM   20  H1  UNL     1       6.526  -3.181  -0.039  1.00  0.00           H  
HETATM   21  H2  UNL     1       6.447  -1.580  -0.814  1.00  0.00           H  
HETATM   22  H3  UNL     1       3.769  -1.017  -1.177  1.00  0.00           H  
HETATM   23  H4  UNL     1       4.430  -0.043   0.230  1.00  0.00           H  
HETATM   24  H5  UNL     1       2.058  -1.950   0.482  1.00  0.00           H  
HETATM   25  H6  UNL     1       2.749  -0.895   1.753  1.00  0.00           H  
HETATM   26  H7  UNL     1       2.278   1.074   0.371  1.00  0.00           H  
HETATM   27  H8  UNL     1       1.512   0.018  -0.872  1.00  0.00           H  
HETATM   28  H9  UNL     1       0.675   0.134   2.074  1.00  0.00           H  
HETATM   29  H10 UNL     1       0.043  -0.947   0.816  1.00  0.00           H  
HETATM   30  H11 UNL     1      -0.558   1.126  -0.566  1.00  0.00           H  
HETATM   31  H12 UNL     1       0.395   2.634   1.891  1.00  0.00           H  
HETATM   32  H13 UNL     1       1.043   2.618   0.211  1.00  0.00           H  
HETATM   33  H14 UNL     1      -1.016   3.505  -0.680  1.00  0.00           H  
HETATM   34  H15 UNL     1      -1.758   3.544   0.980  1.00  0.00           H  
HETATM   35  H16 UNL     1      -0.474   6.159  -0.278  1.00  0.00           H  
HETATM   36  H17 UNL     1      -1.937  -1.693   0.000  1.00  0.00           H  
HETATM   37  H18 UNL     1      -2.391  -0.463  -1.232  1.00  0.00           H  
HETATM   38  H19 UNL     1      -4.235  -2.573   0.085  1.00  0.00           H  
HETATM   39  H20 UNL     1      -3.564  -2.639  -1.564  1.00  0.00           H  
HETATM   40  H21 UNL     1      -6.137  -2.370  -2.406  1.00  0.00           H  
CONECT    1    2   20   21
CONECT    2    3    3    4
CONECT    4    5   22   23
CONECT    5    6   24   25
CONECT    6    7   26   27
CONECT    7    8   28   29
CONECT    8    9   12   30
CONECT    9   10   31   32
CONECT   10   11   33   34
CONECT   11   35
CONECT   12   13
CONECT   13   14   14   15
CONECT   15   16   36   37
CONECT   16   17   38   39
CONECT   17   18   18   19
CONECT   19   40
END

HMDB0001177
     RDKit          3D
(S)-Succinyldihydrolipoamide
 40 39  0  0  0  0  0  0  0  0999 V2000
    6.0119   -2.2906   -0.2168 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7416   -2.1043    0.3712 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3245   -2.8707    1.2636 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9058   -0.9789   -0.0893 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6008   -1.0130    0.6625 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7297    0.1434    0.1937 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4261    0.0472    0.9840 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4854    1.1459    0.5672 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1493    2.5159    0.8388 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8155    3.6155    0.4088 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0922    5.2387    0.7172 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0997    1.1601    1.3061 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1439   -0.1125    0.7196 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2803   -0.2738    1.2055 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7479   -1.0377   -0.3550 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9081   -1.9552   -0.7543 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0080   -1.1186   -1.2274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9549    0.1323   -1.2920 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2093   -1.7048   -1.6428 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5264   -3.1808   -0.0394 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4475   -1.5798   -0.8139 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7691   -1.0169   -1.1771 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4297   -0.0432    0.2301 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0578   -1.9501    0.4824 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7494   -0.8949    1.7535 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2779    1.0743    0.3710 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5122    0.0178   -0.8720 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6754    0.1341    2.0743 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0426   -0.9470    0.8163 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5580    1.1264   -0.5658 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3947    2.6341    1.8912 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0430    2.6178    0.2106 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0164    3.5050   -0.6803 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7579    3.5436    0.9804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4744    6.1594   -0.2779 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9368   -1.6926    0.0004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3908   -0.4634   -1.2318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2348   -2.5727    0.0851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5644   -2.6393   -1.5635 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1368   -2.3704   -2.4058 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  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
  8 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 17 19  1  0
  1 20  1  0
  1 21  1  0
  4 22  1  0
  4 23  1  0
  5 24  1  0
  5 25  1  0
  6 26  1  0
  6 27  1  0
  7 28  1  0
  7 29  1  0
  8 30  1  6
  9 31  1  0
  9 32  1  0
 10 33  1  0
 10 34  1  0
 11 35  1  0
 15 36  1  0
 15 37  1  0
 16 38  1  0
 16 39  1  0
 19 40  1  0
M  END

Synonyms

Value	Source
S-Succinyl-dihydrolipoamide	HMDB
S-Succinyldihydrolipoamide	HMDB

Molecular Formula

C₁₂H₂₁NO₄S₂

Average Mass

307.429

Monoisotopic Mass

307.091199545

IUPAC Name

4-{[(3R)-7-carbamoyl-1-sulfanylheptan-3-yl]sulfanyl}-4-oxobutanoic acid

Traditional Name

4-{[(3R)-7-carbamoyl-1-sulfanylheptan-3-yl]sulfanyl}-4-oxobutanoic acid

CAS Registry Number

Not Available

SMILES

NC(=O)CCCC[C@H](CCS)SC(=O)CCC(O)=O

InChI Identifier

InChI=1S/C12H21NO4S2/c13-10(14)4-2-1-3-9(7-8-18)19-12(17)6-5-11(15)16/h9,18H,1-8H2,(H2,13,14)(H,15,16)/t9-/m1/s1

InChI Key

RJCJWONCSKSHES-SECBINFHSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as thia fatty acids. These are fatty acid derivatives obtained by insertion of a sulfur atom at specific positions in the chain.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Thia fatty acids

Alternative Parents

Substituents

Thia fatty acid
Fatty acyl thioester
Fatty amide
Carboxamide group
Primary carboxylic acid amide
Thiocarboxylic acid ester
Carbothioic s-ester
Sulfenyl compound
Thiocarboxylic acid or derivatives
Alkylthiol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Carbonyl group
Organic oxygen compound
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organic oxide
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.1 g/L	ALOGPS
logP	1.97	ALOGPS
logP	1.06	ChemAxon
logS	-3.5	ALOGPS
pKa (Strongest Acidic)	4.38	ChemAxon
pKa (Strongest Basic)	-0.58	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	97.46 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	78.12 m³·mol⁻¹	ChemAxon
Polarizability	32.86 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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	splash10-0ukc-9880000000-d66345c90ce5eb67fa60	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-00dl-9533000000-a1ebe0f3e16866573001	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 LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0596-0190000000-b49046dab0850898c889	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-006y-2190000000-474bcff100b398100e49	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0nt9-4910000000-247a7886ecdb5a884d7c	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0596-0190000000-b49046dab0850898c889	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-006y-2190000000-474bcff100b398100e49	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0nt9-4910000000-247a7886ecdb5a884d7c	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-5294000000-672a48ef8e666cb0ee5f	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a4j-9360000000-f9e4f05adcb51d48447c	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-000x-9100000000-d7f410ba584f3aad89cc	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-1229000000-d6ef878a291e343f754a	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a4i-7970000000-eff246297f1390d8e037	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-000x-9500000000-66fb2d1c65f8ee705da4	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a4i-0369000000-035798c3620974bb7aab	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03dl-1910000000-e3af53d75b9037036cfe	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udr-5900000000-f70f4c6e3a3b250e485f	2021-09-25	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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
MMDBp0192105	2-oxoglutarate dehydrogenase, mitochondrial	Enzyme	Q02218	Homo sapiens
MMDBp0192557	Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial	Enzyme	P36957	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Data Source	Reference
MMDBr0002528	Oxoglutaric acid	(S)-Succinyldihydrolipoamide	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	VMH	10676873
MMDBr0002597	Dihydrolipoamide	(S)-Succinyldihydrolipoamide	dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarate complex)	VMH	8076640 9620315
MMDBr0002627	3-Carboxy-1-hydroxypropylthiamine diphosphate	(S)-Succinyldihydrolipoamide	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	VMH	10676873
MMDBr0007677	3-Carboxy-1-hydroxypropylthiamine diphosphate	(S)-Succinyldihydrolipoamide	Not Available	VMH	30371894
MMDBr0008015	Dihydrolipoamide	(S)-Succinyldihydrolipoamide	Not Available	VMH	30371894
MMDBr0010914	Dihydrolipoamide	(S)-Succinyldihydrolipoamide	Not Available	VMH	30371894

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
Bacteria	Proteobacteria	148	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal	Unknown; Metabolic reconstruction
Bacteria	Actinobacteria	49	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human mucosa; Human supragingival plaque; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Firmicutes	66	Human feces; Human ; Human subgingival plaque	Metabolic reconstruction
Bacteria	Bacteroidetes	8	Human feces; Human ; Human supragingival plaque; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction

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
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0001177

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022467

KNApSAcK ID

Not Available

Chemspider ID

388536

KEGG Compound ID

C01169

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

6058

PubChem Compound

439425

PDB ID

Not Available

ChEBI ID

17432

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]

Showing metabocard for (S)-Succinyldihydrolipoamide (MMDBc0031895)

MOL for #<Metabolite:0x00005634c289ace0>

3D MOL for #<Metabolite:0x00005634c289ace0>

3D SDF for #<Metabolite:0x00005634c289ace0>

3D-SDF for #<Metabolite:0x00005634c289ace0>

PDB for #<Metabolite:0x00005634c289ace0>

3D PDB for #<Metabolite:0x00005634c289ace0>

SMILES for #<Metabolite:0x00005634c289ace0>

INCHI for #<Metabolite:0x00005634c289ace0>

Structure for #<Metabolite:0x00005634c289ace0>

3D Structure for #<Metabolite:0x00005634c289ace0>