Showing metabocard for (S)-5-Amino-3-oxohexanoate (MMDBc0049860)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-04-29 22:44:57 UTC
Update Date2025-01-15 22:43:04 UTC
Metabolite IDMMDBc0049860
Metabolite Identification
Common Name(S)-5-Amino-3-oxohexanoate
Description(S)-5-Amino-3-oxohexanoate is an intermediate in lysine degradation. L-Lysine is an essential amino acid that is a necessary building block for all protein in the body and It plays a major role in calcium absorption; building muscle protein; recovering from surgery or sports injuries; and the body's production of hormones, enzymes, and antibodies. In lysine degradation pathway, (S)-5-Amino-3-oxohexanoate is a substrate for the enzyme L-erythro-3,5-diaminohexanoate dehydrogenase (EC 1.4.1.11) and can be generated from L-erythro-3,5-Diaminohexanoate.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f5358a06e98>


  Mrv0541 02241203462D          

 10  9  0  0  1  0            999 V2000
   14.5679  -12.8300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8053  -12.1154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0428  -11.4008    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.3929  -12.8300    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.6303  -12.1154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6303  -10.6869    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8053  -13.5445    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.0428  -12.8300    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.0428   -9.9723    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.8053  -10.6869    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  1  0  0  0
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  4  7  1  0  0  0  0
  5  8  2  0  0  0  0
  6  9  1  0  0  0  0
  6 10  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f5358a06e98>

HMDB0012131
     RDKit          3D
(S)-5-Amino-3-oxohexanoate
 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.9306   -0.3812    0.0185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5378   -0.0369    0.5138 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4154    1.4224    0.5175 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4673   -0.5803   -0.3750 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8614   -0.1900    0.1924 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9308    0.4626    1.2098 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1074   -0.6253   -0.5290 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2660   -0.1126    0.2281 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6342   -0.7282    1.2531 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9360    1.0205   -0.1763 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6231    0.4405    0.2888 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2975   -1.2821    0.5546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9239   -0.5888   -1.0636 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4574   -0.3763    1.5529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3275    1.6986   -0.4973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3023    1.8696    0.8674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5512   -0.1169   -1.3764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4998   -1.6769   -0.4711 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0658   -0.2536   -1.5689 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0904   -1.7545   -0.4944 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4417    1.7896   -0.6451 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  1
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  7 19  1  0
  7 20  1  0
 10 21  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f5358a06e98>


  Mrv0541 02241203462D          

 10  9  0  0  1  0            999 V2000
   14.5679  -12.8300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8053  -12.1154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0428  -11.4008    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.3929  -12.8300    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.6303  -12.1154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6303  -10.6869    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8053  -13.5445    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.0428  -12.8300    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.0428   -9.9723    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.8053  -10.6869    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  1  0  0  0
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  4  7  1  0  0  0  0
  5  8  2  0  0  0  0
  6  9  1  0  0  0  0
  6 10  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0049860

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H11NO3/c1-4(7)2-5(8)3-6(9)10/h4H,2-3,7H2,1H3,(H,9,10)/t4-/m0/s1

> <INCHI_KEY>
FAASBXNEOGMQHS-BYPYZUCNSA-N

> <FORMULA>
C6H11NO3

> <MOLECULAR_WEIGHT>
145.1564

> <EXACT_MASS>
145.073893223

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
14.244018502988348

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(5S)-5-amino-3-oxohexanoic acid

> <ALOGPS_LOGP>
-2.45

> <JCHEM_LOGP>
-2.5354565104937414

> <ALOGPS_LOGS>
-0.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.343774847547579

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.078848716633465

> <JCHEM_PKA_STRONGEST_BASIC>
9.890138246532258

> <JCHEM_POLAR_SURFACE_AREA>
80.39000000000001

> <JCHEM_REFRACTIVITY>
35.0168

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.43e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(S)-5-amino-3-oxohexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f5358a06e98>

HMDB0012131
     RDKit          3D
(S)-5-Amino-3-oxohexanoate
 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.9306   -0.3812    0.0185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5378   -0.0369    0.5138 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4154    1.4224    0.5175 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4673   -0.5803   -0.3750 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8614   -0.1900    0.1924 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9308    0.4626    1.2098 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1074   -0.6253   -0.5290 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2660   -0.1126    0.2281 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6342   -0.7282    1.2531 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9360    1.0205   -0.1763 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6231    0.4405    0.2888 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2975   -1.2821    0.5546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9239   -0.5888   -1.0636 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4574   -0.3763    1.5529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3275    1.6986   -0.4973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3023    1.8696    0.8674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5512   -0.1169   -1.3764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4998   -1.6769   -0.4711 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0658   -0.2536   -1.5689 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0904   -1.7545   -0.4944 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4417    1.7896   -0.6451 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  1
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  7 19  1  0
  7 20  1  0
 10 21  1  0
M  END
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PDB for #<Metabolite:0x00007f5358a06e98>

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      27.193 -23.949   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      29.503 -22.615   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      31.813 -21.281   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      28.733 -23.949   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      31.043 -22.615   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      31.043 -19.949   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      29.503 -25.283   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0      31.813 -23.949   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      31.813 -18.615   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      29.503 -19.949   0.000  0.00  0.00           O+0
CONECT    1    4                                                            
CONECT    2    4    5                                                       
CONECT    3    5    6                                                       
CONECT    4    1    2    7                                                  
CONECT    5    2    3    8                                                  
CONECT    6    3    9   10                                                  
CONECT    7    4                                                            
CONECT    8    5                                                            
CONECT    9    6                                                            
CONECT   10    6                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for #<Metabolite:0x00007f5358a06e98>

COMPND    HMDB0012131
HETATM    1  C1  UNL     1      -2.931  -0.381   0.018  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.538  -0.037   0.514  1.00  0.00           C  
HETATM    3  N1  UNL     1      -1.415   1.422   0.517  1.00  0.00           N  
HETATM    4  C3  UNL     1      -0.467  -0.580  -0.375  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.861  -0.190   0.192  1.00  0.00           C  
HETATM    6  O1  UNL     1       0.931   0.463   1.210  1.00  0.00           O  
HETATM    7  C5  UNL     1       2.107  -0.625  -0.529  1.00  0.00           C  
HETATM    8  C6  UNL     1       3.266  -0.113   0.228  1.00  0.00           C  
HETATM    9  O2  UNL     1       3.634  -0.728   1.253  1.00  0.00           O  
HETATM   10  O3  UNL     1       3.936   1.020  -0.176  1.00  0.00           O  
HETATM   11  H1  UNL     1      -3.623   0.441   0.289  1.00  0.00           H  
HETATM   12  H2  UNL     1      -3.298  -1.282   0.555  1.00  0.00           H  
HETATM   13  H3  UNL     1      -2.924  -0.589  -1.064  1.00  0.00           H  
HETATM   14  H4  UNL     1      -1.457  -0.376   1.553  1.00  0.00           H  
HETATM   15  H5  UNL     1      -1.327   1.699  -0.497  1.00  0.00           H  
HETATM   16  H6  UNL     1      -2.302   1.870   0.867  1.00  0.00           H  
HETATM   17  H7  UNL     1      -0.551  -0.117  -1.376  1.00  0.00           H  
HETATM   18  H8  UNL     1      -0.500  -1.677  -0.471  1.00  0.00           H  
HETATM   19  H9  UNL     1       2.066  -0.254  -1.569  1.00  0.00           H  
HETATM   20  H10 UNL     1       2.090  -1.755  -0.494  1.00  0.00           H  
HETATM   21  H11 UNL     1       3.442   1.790  -0.645  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3    4   14
CONECT    3   15   16
CONECT    4    5   17   18
CONECT    5    6    6    7
CONECT    7    8   19   20
CONECT    8    9    9   10
CONECT   10   21
END
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SMILES for #<Metabolite:0x00007f5358a06e98>

C[C@H](N)CC(=O)CC(O)=O
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INCHI for #<Metabolite:0x00007f5358a06e98>

InChI=1S/C6H11NO3/c1-4(7)2-5(8)3-6(9)10/h4H,2-3,7H2,1H3,(H,9,10)/t4-/m0/s1
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Synonyms
ValueSource
(S)-5-Amino-3-oxohexanoic acidGenerator
(S)-5-amino-3-oxo-Hexanoic acidChEBI, HMDB
(S)-5-amino-3-oxo-HexanoateGenerator, HMDB
3-keto-5-AminohexanoateHMDB, MeSH
3-keto-5-Aminohexanoic acidHMDB
5-amino-3-OxohexanoateHMDB
5-amino-3-Oxohexanoic acidHMDB
(S)-5-Amino-3-oxohexanoateChEBI
3-oxo-5S-Amino-hexanoateGenerator, HMDB
Molecular FormulaC6H11NO3
Average Mass145.1564
Monoisotopic Mass145.073893223
IUPAC Name(5S)-5-amino-3-oxohexanoic acid
Traditional Name(S)-5-amino-3-oxohexanoic acid
CAS Registry Number19355-90-9
SMILES
C[C@H](N)CC(=O)CC(O)=O
InChI Identifier
InChI=1S/C6H11NO3/c1-4(7)2-5(8)3-6(9)10/h4H,2-3,7H2,1H3,(H,9,10)/t4-/m0/s1
InChI KeyFAASBXNEOGMQHS-BYPYZUCNSA-N