NP-MRD: Showing NP-Card for Saccharopine (NP0001133)

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Record Information

Version

1.0

Created at

2005-11-16 15:48:42 UTC

Updated at

2020-11-24 22:21:03 UTC

NP-MRD ID

NP0001133

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Saccharopine

Description

Saccharopine is an intermediate in the degradation of lysine, formed by the condensation of lysine and alpha-ketoglutarate. The saccharopine pathway is the main route for lysine degradation in mammals, and its first two reactions are catalyzed by enzymatic activities known as lysine-oxoglutarate reductase (LOR) and saccharopine dehydrogenase (SDH), which reside on a single bifunctional polypeptide (LOR/SDH) (EC 1.5.1.8). The reactions involved with saccharopine dehydrogenases have very strict substrate specificity for L-lysine, 2-oxoglutarate, and NADPH. LOR/SDH has been detected in a number of mammalian tissues, mainly in the liver and kidney, contributing not only to the general nitrogen balance in the organism but also to the controlled conversion of lysine into ketone bodies. A tetrameric form has also been observed in human liver and placenta. LOR activity has also been detected in brain mitochondria during embryonic development, and this opens up the question of whether or not lysine degradation has any functional significance during brain development. As a result, there is now a new focus on the nutritional requirements for lysine in gestation and infancy. Finally, LOR and/or SDH deficiencies seem to be involved in a human autosomal genetic disorder known as familial hyperlysinemia, which is characterized by serious defects in the functioning of the nervous system and characterized by a deficiency in lysine-ketoglutarate reductase, saccharopine dehydrogenase, and saccharopine oxidoreductase activities. Saccharopinuria (high amounts of saccharopine in the urine) and saccharopinemia (an excess of saccharopine in the blood) are conditions present in some inherited disorders of lysine degradation (PMID: 463877 , 10567240 , 10772957 , 4809305 ). If present in sufficiently high levels, saccharopine can act as an acidogen and a metabotoxin. An acidogen is an acidic compound that induces acidosis, which has multiple adverse effects on many organ systems. A metabotoxin is an endogenously produced metabolite that causes adverse health effects at chronically high levels. Saccharopine is an organic acid. Abnormally high levels of organic acids in the blood (organic acidemia), urine (organic aciduria), the brain, and other tissues lead to general metabolic acidosis. Acidosis typically occurs when arterial pH falls below 7.35. In infants with acidosis, the initial symptoms include poor feeding, vomiting, loss of appetite, weak muscle tone (hypotonia), and lack of energy (lethargy). Many affected children with organic acidemias experience intellectual disability or delayed development.

Structure

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

HMDB0000279
     RDKit          3D
Saccharopine
 39 38  0  0  0  0  0  0  0  0999 V2000
   -4.2431    0.6793   -0.9565 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0850   -0.4854   -0.0994 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2506   -0.1163    1.1048 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8710    0.3755    0.7273 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1627   -0.7054   -0.0150 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2366   -0.3090   -0.4406 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0706    0.0188    0.6578 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4078    0.4160    0.2516 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1025   -0.6496   -0.5079 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5014   -0.2917   -0.8962 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3694   -0.0549    0.2769 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3377    1.0090    0.8965 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2573   -1.0393    0.7199 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4093    1.6983   -0.4581 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2763    2.3087   -0.5473 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4659    2.3388   -1.0445 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4111   -0.9346    0.4117 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4994   -1.9165    1.1628 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5313   -0.2446    0.0379 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1532    1.1494   -0.7281 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2920    0.3515   -1.9368 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6729   -1.3292   -0.6786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8229    0.6293    1.6886 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1570   -1.0500    1.7160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9967    1.2983    0.1298 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3656    0.6306    1.6914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7233   -0.8533   -0.9839 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1430   -1.6279    0.5590 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6580   -1.2697   -0.8804 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2128    0.4707   -1.1929 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6890    0.8355    1.2207 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0151    0.6001    1.1971 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1968   -1.6042    0.0924 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5681   -0.8730   -1.4738 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5772    0.4794   -1.6846 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9460   -1.2153   -1.4036 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0307   -2.0368    0.6315 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1116    2.9655   -0.6300 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0593    0.3519    0.6454 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  2  0
 11 13  1  0
  8 14  1  0
 14 15  2  0
 14 16  1  0
  2 17  1  0
 17 18  2  0
 17 19  1  0
  1 20  1  0
  1 21  1  0
  2 22  1  6
  3 23  1  0
  3 24  1  0
  4 25  1  0
  4 26  1  0
  5 27  1  0
  5 28  1  0
  6 29  1  0
  6 30  1  0
  7 31  1  0
  8 32  1  1
  9 33  1  0
  9 34  1  0
 10 35  1  0
 10 36  1  0
 13 37  1  0
 16 38  1  0
 19 39  1  0
M  END


  Mrv1652309032023592D          

 19 18  0  0  0  0            999 V2000
10001.123310002.5437    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10000.408510002.9560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.693910002.5437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.979210002.9560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.264610002.5437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.979210003.7807    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.837910002.9560    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
10002.552410002.5437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.266810002.9560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.984310002.5437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10004.697710002.9560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10005.413110002.5437    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10006.128510002.9560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10006.841910002.5437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10006.128510003.7807    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10005.413110001.7194    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
10001.123310001.7194    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.408510001.3058    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.837910001.3058    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  7  1  0  0  0  0
  1 17  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  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  0  0  0  0
 12 13  1  0  0  0  0
 12 16  1  1  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0001133

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N[C@@H](CCCCN[C@@H](CCC(O)=O)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H20N2O6/c12-7(10(16)17)3-1-2-6-13-8(11(18)19)4-5-9(14)15/h7-8,13H,1-6,12H2,(H,14,15)(H,16,17)(H,18,19)/t7-,8-/m0/s1

> <INCHI_KEY>
ZDGJAHTZVHVLOT-YUMQZZPRSA-N

> <FORMULA>
C11H20N2O6

> <MOLECULAR_WEIGHT>
276.2863

> <EXACT_MASS>
276.132136382

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
28.138708375547512

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-{[(5S)-5-amino-5-carboxypentyl]amino}pentanedioic acid

> <ALOGPS_LOGP>
-2.77

> <JCHEM_LOGP>
-5.407435330625966

> <ALOGPS_LOGS>
-1.72

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
2.375174811126724

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4444535649435268

> <JCHEM_PKA_STRONGEST_BASIC>
10.892138404544818

> <JCHEM_POLAR_SURFACE_AREA>
149.95

> <JCHEM_REFRACTIVITY>
63.95300000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.25e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
saccharopine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000279
     RDKit          3D
Saccharopine
 39 38  0  0  0  0  0  0  0  0999 V2000
   -4.2431    0.6793   -0.9565 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0850   -0.4854   -0.0994 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2506   -0.1163    1.1048 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8710    0.3755    0.7273 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1627   -0.7054   -0.0150 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2366   -0.3090   -0.4406 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0706    0.0188    0.6578 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4078    0.4160    0.2516 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1025   -0.6496   -0.5079 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5014   -0.2917   -0.8962 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3694   -0.0549    0.2769 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3377    1.0090    0.8965 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2573   -1.0393    0.7199 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4093    1.6983   -0.4581 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2763    2.3087   -0.5473 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4659    2.3388   -1.0445 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4111   -0.9346    0.4117 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4994   -1.9165    1.1628 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5313   -0.2446    0.0379 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1532    1.1494   -0.7281 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2920    0.3515   -1.9368 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6729   -1.3292   -0.6786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8229    0.6293    1.6886 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1570   -1.0500    1.7160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9967    1.2983    0.1298 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3656    0.6306    1.6914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7233   -0.8533   -0.9839 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1430   -1.6279    0.5590 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6580   -1.2697   -0.8804 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2128    0.4707   -1.1929 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6890    0.8355    1.2207 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0151    0.6001    1.1971 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1968   -1.6042    0.0924 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5681   -0.8730   -1.4738 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5772    0.4794   -1.6846 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9460   -1.2153   -1.4036 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0307   -2.0368    0.6315 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1116    2.9655   -0.6300 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0593    0.3519    0.6454 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  2  0
 11 13  1  0
  8 14  1  0
 14 15  2  0
 14 16  1  0
  2 17  1  0
 17 18  2  0
 17 19  1  0
  1 20  1  0
  1 21  1  0
  2 22  1  6
  3 23  1  0
  3 24  1  0
  4 25  1  0
  4 26  1  0
  5 27  1  0
  5 28  1  0
  6 29  1  0
  6 30  1  0
  7 31  1  0
  8 32  1  1
  9 33  1  0
  9 34  1  0
 10 35  1  0
 10 36  1  0
 13 37  1  0
 16 38  1  0
 19 39  1  0
M  END

HEADER    PROTEIN                                 03-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-20         0                                  
HETATM    1  C   UNK     0    8668.7638671.415   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8667.4298672.185   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8666.0958671.415   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8664.7618672.185   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0    8663.4278671.415   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8664.7618673.724   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0    8670.0978672.185   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0    8671.4318671.415   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8672.7658672.185   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8674.1048671.415   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8675.4368672.185   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8676.7718671.415   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8678.1078672.185   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0    8679.4388671.415   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0    8678.1078673.724   0.000  0.00  0.00           O+0
HETATM   16  N   UNK     0    8676.7718669.876   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0    8668.7638669.876   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0    8667.4298669.104   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0    8670.0978669.104   0.000  0.00  0.00           O+0
CONECT    1    2    7   17                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    1    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   16                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   12                                                            
CONECT   17    1   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   36    0
END

COMPND    HMDB0000279
HETATM    1  N1  UNL     1      -4.243   0.679  -0.956  1.00  0.00           N  
HETATM    2  C1  UNL     1      -4.085  -0.485  -0.099  1.00  0.00           C  
HETATM    3  C2  UNL     1      -3.251  -0.116   1.105  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.871   0.376   0.727  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.163  -0.705  -0.015  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.237  -0.309  -0.441  1.00  0.00           C  
HETATM    7  N2  UNL     1       1.071   0.019   0.658  1.00  0.00           N  
HETATM    8  C6  UNL     1       2.408   0.416   0.252  1.00  0.00           C  
HETATM    9  C7  UNL     1       3.102  -0.650  -0.508  1.00  0.00           C  
HETATM   10  C8  UNL     1       4.501  -0.292  -0.896  1.00  0.00           C  
HETATM   11  C9  UNL     1       5.369  -0.055   0.277  1.00  0.00           C  
HETATM   12  O1  UNL     1       5.338   1.009   0.896  1.00  0.00           O  
HETATM   13  O2  UNL     1       6.257  -1.039   0.720  1.00  0.00           O  
HETATM   14  C10 UNL     1       2.409   1.698  -0.458  1.00  0.00           C  
HETATM   15  O3  UNL     1       1.276   2.309  -0.547  1.00  0.00           O  
HETATM   16  O4  UNL     1       3.466   2.339  -1.045  1.00  0.00           O  
HETATM   17  C11 UNL     1      -5.411  -0.935   0.412  1.00  0.00           C  
HETATM   18  O5  UNL     1      -5.499  -1.916   1.163  1.00  0.00           O  
HETATM   19  O6  UNL     1      -6.531  -0.245   0.038  1.00  0.00           O  
HETATM   20  H1  UNL     1      -5.153   1.149  -0.728  1.00  0.00           H  
HETATM   21  H2  UNL     1      -4.292   0.351  -1.937  1.00  0.00           H  
HETATM   22  H3  UNL     1      -3.673  -1.329  -0.679  1.00  0.00           H  
HETATM   23  H4  UNL     1      -3.823   0.629   1.689  1.00  0.00           H  
HETATM   24  H5  UNL     1      -3.157  -1.050   1.716  1.00  0.00           H  
HETATM   25  H6  UNL     1      -1.997   1.298   0.130  1.00  0.00           H  
HETATM   26  H7  UNL     1      -1.366   0.631   1.691  1.00  0.00           H  
HETATM   27  H8  UNL     1      -1.723  -0.853  -0.984  1.00  0.00           H  
HETATM   28  H9  UNL     1      -1.143  -1.628   0.559  1.00  0.00           H  
HETATM   29  H10 UNL     1       0.658  -1.270  -0.880  1.00  0.00           H  
HETATM   30  H11 UNL     1       0.213   0.471  -1.193  1.00  0.00           H  
HETATM   31  H12 UNL     1       0.689   0.836   1.221  1.00  0.00           H  
HETATM   32  H13 UNL     1       3.015   0.600   1.197  1.00  0.00           H  
HETATM   33  H14 UNL     1       3.197  -1.604   0.092  1.00  0.00           H  
HETATM   34  H15 UNL     1       2.568  -0.873  -1.474  1.00  0.00           H  
HETATM   35  H16 UNL     1       4.577   0.479  -1.685  1.00  0.00           H  
HETATM   36  H17 UNL     1       4.946  -1.215  -1.404  1.00  0.00           H  
HETATM   37  H18 UNL     1       6.031  -2.037   0.631  1.00  0.00           H  
HETATM   38  H19 UNL     1       4.112   2.966  -0.630  1.00  0.00           H  
HETATM   39  H20 UNL     1      -7.059   0.352   0.645  1.00  0.00           H  
CONECT    1    2   20   21
CONECT    2    3   17   22
CONECT    3    4   23   24
CONECT    4    5   25   26
CONECT    5    6   27   28
CONECT    6    7   29   30
CONECT    7    8   31
CONECT    8    9   14   32
CONECT    9   10   33   34
CONECT   10   11   35   36
CONECT   11   12   12   13
CONECT   13   37
CONECT   14   15   15   16
CONECT   16   38
CONECT   17   18   18   19
CONECT   19   39
END

HMDB0000279
     RDKit          3D
Saccharopine
 39 38  0  0  0  0  0  0  0  0999 V2000
   -4.2431    0.6793   -0.9565 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0850   -0.4854   -0.0994 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2506   -0.1163    1.1048 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8710    0.3755    0.7273 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1627   -0.7054   -0.0150 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2366   -0.3090   -0.4406 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0706    0.0188    0.6578 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4078    0.4160    0.2516 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1025   -0.6496   -0.5079 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5014   -0.2917   -0.8962 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3694   -0.0549    0.2769 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3377    1.0090    0.8965 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2573   -1.0393    0.7199 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4093    1.6983   -0.4581 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2763    2.3087   -0.5473 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4659    2.3388   -1.0445 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4111   -0.9346    0.4117 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4994   -1.9165    1.1628 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5313   -0.2446    0.0379 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1532    1.1494   -0.7281 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2920    0.3515   -1.9368 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6729   -1.3292   -0.6786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8229    0.6293    1.6886 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1570   -1.0500    1.7160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9967    1.2983    0.1298 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3656    0.6306    1.6914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7233   -0.8533   -0.9839 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1430   -1.6279    0.5590 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6580   -1.2697   -0.8804 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2128    0.4707   -1.1929 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6890    0.8355    1.2207 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0151    0.6001    1.1971 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1968   -1.6042    0.0924 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5681   -0.8730   -1.4738 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5772    0.4794   -1.6846 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9460   -1.2153   -1.4036 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0307   -2.0368    0.6315 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1116    2.9655   -0.6300 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0593    0.3519    0.6454 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  2  0
 11 13  1  0
  8 14  1  0
 14 15  2  0
 14 16  1  0
  2 17  1  0
 17 18  2  0
 17 19  1  0
  1 20  1  0
  1 21  1  0
  2 22  1  6
  3 23  1  0
  3 24  1  0
  4 25  1  0
  4 26  1  0
  5 27  1  0
  5 28  1  0
  6 29  1  0
  6 30  1  0
  7 31  1  0
  8 32  1  1
  9 33  1  0
  9 34  1  0
 10 35  1  0
 10 36  1  0
 13 37  1  0
 16 38  1  0
 19 39  1  0
M  END

View in JSmol

Synonyms

Value	Source
epsilon-N-(L-Glutar-2-yl)-L-lysine	ChEBI
N-[(S)-5-Amino-5-carboxypentyl]-L-glutamic acid	ChEBI
N6-(L-1,3-Dicarboxypropyl)-L-lysine	ChEBI
L-Saccharopine	Kegg
N-[(S)-5-Amino-5-carboxypentyl]-L-glutamate	Generator
(S)-N-(5-Amino-5-carboxypentyl)-L-glutamic acid	HMDB
L-N-(5-Amino-5-carboxypentyl)-glutamic acid	HMDB
L-Saccharopin	HMDB
N(6)-(L-1,3-Dicarboxypropyl)-L-lysine	HMDB
N-(5-Amino-5-carboxypentyl)-glutamic acid	HMDB
N-(5-Amino-5-carboxypentyl)-L-glutamic acid	HMDB
N-[(5S)-5-Amino-5-carboxypentyl]-L-glutamic acid	HMDB
Saccharopin	HMDB

Chemical Formula

C₁₁H₂₀N₂O₆

Average Mass

276.2863 Da

Monoisotopic Mass

276.13214 Da

IUPAC Name

(2S)-2-{[(5S)-5-amino-5-carboxypentyl]amino}pentanedioic acid

Traditional Name

saccharopine

CAS Registry Number

997-68-2

SMILES

N[C@@H](CCCCN[C@@H](CCC(O)=O)C(O)=O)C(O)=O

InChI Identifier

InChI=1S/C11H20N2O6/c12-7(10(16)17)3-1-2-6-13-8(11(18)19)4-5-9(14)15/h7-8,13H,1-6,12H2,(H,14,15)(H,16,17)(H,18,19)/t7-,8-/m0/s1

InChI Key

ZDGJAHTZVHVLOT-YUMQZZPRSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Agaricus bisporus	LOTUS Database	35616633
Alternaria oxytropis	-	KNApSAcK
Apis cerana	LOTUS Database	35616633
Arabidopsis thaliana	KNApSAcK Database	22123792
Cannabis sativa	CannabisDB	Not Available
Caylusea abyssinica	LOTUS Database	35616633
Flammulina velutipes	LOTUS Database	35616633
Nicotiana tabacum	KNApSAcK Database	22123792
Psophocarpus tetragonolobus	LOTUS Database	35616633
Vigna radiata	LOTUS Database	35616633

Species Where Detected

Species Name	Source	Reference
Lentinus edodes	KNApSAcK Database	22123792

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glutamic acid and derivatives. Glutamic acid and derivatives are compounds containing glutamic acid or a derivative thereof resulting from reaction of glutamic acid at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Glutamic acid and derivatives

Alternative Parents

Substituents

Glutamic acid or derivatives
Alpha-amino acid
L-alpha-amino acid
Tricarboxylic acid or derivatives
Amino fatty acid
Fatty acyl
Amino acid
Carboxylic acid
Secondary aliphatic amine
Secondary amine
Amine
Primary amine
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Organic nitrogen compound
Carbonyl group
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

L-lysine derivative (CHEBI:16927 )
amino acid opine (CHEBI:16927 )

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	247 - 250 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	5.25 g/L	ALOGPS
logP	-2.8	ALOGPS
logP	-5.4	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	1.44	ChemAxon
pKa (Strongest Basic)	10.89	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	149.95 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	63.95 m³·mol⁻¹	ChemAxon
Polarizability	28.14 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0000279

DrugBank ID

DB04207

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

16927

Good Scents ID

Not Available

References

General References

IJlst L, de Kromme I, Oostheim W, Wanders RJ: Molecular cloning and expression of human L-pipecolate oxidase. Biochem Biophys Res Commun. 2000 Apr 21;270(3):1101-5. [PubMed:10772957 ]
Krieger I, Bachmann C, Gronemeyer WH, Cejka J: Propionic acidemia and hyperlysinemia in a case with ornithine transcarbamylase (OTC) deficiency. J Clin Endocrinol Metab. 1976 Oct;43(4):796-802. [PubMed:977722 ]
Cederbaum SD, Shaw KN, Dancis J, Hutzler J, Blaskovics JC: Hyperlysinemia with saccharopinuria due to combined lysine-ketoglutarate reductase and saccharopine dehydrogenase deficiencies presenting as cystinuria. J Pediatr. 1979 Aug;95(2):234-8. [PubMed:571908 ]
Casey RE, Zaleski WA, Philp M, Mendelson IS, MacKenzie SL: Biochemical and clinical studies of a new case of alpha-aminoadipic aciduria. J Inherit Metab Dis. 1978;1(4):129-35. [PubMed:117247 ]
Fellows FC, Carson NA: Enzyme studies in a patient with saccharopinuria: a defect of lysine metabolism. Pediatr Res. 1974 Jan;8(1):42-9. [PubMed:4809305 ]
Dancis J, Hutzler J, Cox RP: Familial hyperlysinemia: enzyme studies, diagnostic methods, comments on terminology. Am J Hum Genet. 1979 May;31(3):290-9. [PubMed:463877 ]
Papes F, Kemper EL, Cord-Neto G, Langone F, Arruda P: Lysine degradation through the saccharopine pathway in mammals: involvement of both bifunctional and monofunctional lysine-degrading enzymes in mouse. Biochem J. 1999 Dec 1;344 Pt 2:555-63. [PubMed:10567240 ]

Showing NP-Card for Saccharopine (NP0001133)

MOL for NP0001133 (Saccharopine)

3D MOL for NP0001133 (Saccharopine)

3D SDF for NP0001133 (Saccharopine)

3D-SDF for NP0001133 (Saccharopine)

PDB for NP0001133 (Saccharopine)

3D PDB for NP0001133 (Saccharopine)

SMILES for NP0001133 (Saccharopine)

INCHI for NP0001133 (Saccharopine)

Structure for NP0001133 (Saccharopine)

3D Structure for NP0001133 (Saccharopine)