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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 23:46:40 UTC

Update Date

2021-09-26 22:56:03 UTC

HMDB ID

HMDB0246764

Secondary Accession Numbers

None

Metabolite Identification

Common Name

5-(delta-Carboxybutyl)homocysteine

Description

5-(delta-Carboxybutyl)homocysteine belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). Based on a literature review a small amount of articles have been published on 5-(delta-Carboxybutyl)homocysteine. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5-(delta-carboxybutyl)homocysteine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5-(delta-Carboxybutyl)homocysteine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

HMDB0246764
     RDKit          3D
5-(delta-Carboxybutyl)homocysteine
 29 28  0  0  0  0  0  0  0  0999 V2000
    3.7381   -1.2883    0.2919 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3050    0.0241    0.6634 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8077    0.1985    0.5733 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2973   -0.0361   -0.8269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4984    0.1735   -0.9276 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2789   -1.1429    0.0486 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7881   -1.0343    0.0116 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2653    0.2882    0.5705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7461    0.3160    0.5000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4010   -0.6542    0.0327 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4005    1.4532    0.9685 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9194    1.0387   -0.2284 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6927    0.6802   -1.1455 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6393    2.3839   -0.0490 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0215   -1.2517   -0.7181 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9240   -1.9521    0.3248 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6683    0.2204    1.6921 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3527   -0.5247    1.2806 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5173    1.2145    0.9083 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8372    0.5517   -1.5657 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5067   -1.1162   -1.0653 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9723   -0.9652    1.1132 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9261   -2.1397   -0.2215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1689   -1.2037   -1.0144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2068   -1.8330    0.6566 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8661    1.1187   -0.0557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9394    0.4413    1.6043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0292    2.3501    0.6748 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2601    2.6891    0.8306 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  2  0
  9 11  1  0
  2 12  1  0
 12 13  2  0
 12 14  1  0
  1 15  1  0
  1 16  1  0
  2 17  1  0
  3 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
  8 26  1  0
  8 27  1  0
 11 28  1  0
 14 29  1  0
M  END


  Mrv1652309112101462D          

 14 13  0  0  0  0            999 V2000
    6.3789    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6645    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9500    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2355    3.2704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9500    2.0329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0934    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8079    2.8579    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    8.5224    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2368    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9513    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6658    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3802    3.2704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6658    2.0329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.9513    4.0954    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  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  2  0  0  0  0
 11 13  1  0  0  0  0
 10 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0246764

> <DATABASE_NAME>
hmdb

> <SMILES>
NC(CCSCCCC(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H15NO4S/c9-6(8(12)13)3-5-14-4-1-2-7(10)11/h6H,1-5,9H2,(H,10,11)(H,12,13)

> <INCHI_KEY>
GAWAENRCVHPTKZ-UHFFFAOYSA-N

> <FORMULA>
C8H15NO4S

> <MOLECULAR_WEIGHT>
221.27

> <EXACT_MASS>
221.072179141

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
23.091571525507238

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-amino-4-[(3-carboxypropyl)sulfanyl]butanoic acid

> <ALOGPS_LOGP>
-2.27

> <JCHEM_LOGP>
-2.3412342069274823

> <ALOGPS_LOGS>
-1.69

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.516718716805126

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.0721458962883488

> <JCHEM_PKA_STRONGEST_BASIC>
9.502320710145245

> <JCHEM_POLAR_SURFACE_AREA>
100.61999999999999

> <JCHEM_REFRACTIVITY>
53.1742

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.53e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-amino-4-[(3-carboxypropyl)sulfanyl]butanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0246764
     RDKit          3D
5-(delta-Carboxybutyl)homocysteine
 29 28  0  0  0  0  0  0  0  0999 V2000
    3.7381   -1.2883    0.2919 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3050    0.0241    0.6634 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8077    0.1985    0.5733 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2973   -0.0361   -0.8269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4984    0.1735   -0.9276 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2789   -1.1429    0.0486 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7881   -1.0343    0.0116 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2653    0.2882    0.5705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7461    0.3160    0.5000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4010   -0.6542    0.0327 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4005    1.4532    0.9685 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9194    1.0387   -0.2284 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6927    0.6802   -1.1455 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6393    2.3839   -0.0490 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0215   -1.2517   -0.7181 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9240   -1.9521    0.3248 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6683    0.2204    1.6921 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3527   -0.5247    1.2806 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5173    1.2145    0.9083 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8372    0.5517   -1.5657 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5067   -1.1162   -1.0653 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9723   -0.9652    1.1132 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9261   -2.1397   -0.2215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1689   -1.2037   -1.0144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2068   -1.8330    0.6566 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8661    1.1187   -0.0557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9394    0.4413    1.6043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0292    2.3501    0.6748 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2601    2.6891    0.8306 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  2  0
  9 11  1  0
  2 12  1  0
 12 13  2  0
 12 14  1  0
  1 15  1  0
  1 16  1  0
  2 17  1  0
  3 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
  8 26  1  0
  8 27  1  0
 11 28  1  0
 14 29  1  0
M  END

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0      11.907   5.335   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.574   6.105   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.240   5.335   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       7.906   6.105   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       9.240   3.795   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      13.241   6.105   0.000  0.00  0.00           C+0
HETATM    7  S   UNK     0      14.575   5.335   0.000  0.00  0.00           S+0
HETATM    8  C   UNK     0      15.908   6.105   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      17.242   5.335   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      18.576   6.105   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      19.909   5.335   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      21.243   6.105   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      19.909   3.795   0.000  0.00  0.00           O+0
HETATM   14  N   UNK     0      18.576   7.645   0.000  0.00  0.00           N+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    1    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   14                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   10                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

COMPND    HMDB0246764
HETATM    1  N1  UNL     1       3.738  -1.288   0.292  1.00  0.00           N  
HETATM    2  C1  UNL     1       3.305   0.024   0.663  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.808   0.199   0.573  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.297  -0.036  -0.827  1.00  0.00           C  
HETATM    5  S1  UNL     1      -0.498   0.173  -0.928  1.00  0.00           S  
HETATM    6  C4  UNL     1      -1.279  -1.143   0.049  1.00  0.00           C  
HETATM    7  C5  UNL     1      -2.788  -1.034   0.012  1.00  0.00           C  
HETATM    8  C6  UNL     1      -3.265   0.288   0.571  1.00  0.00           C  
HETATM    9  C7  UNL     1      -4.746   0.316   0.500  1.00  0.00           C  
HETATM   10  O1  UNL     1      -5.401  -0.654   0.033  1.00  0.00           O  
HETATM   11  O2  UNL     1      -5.401   1.453   0.969  1.00  0.00           O  
HETATM   12  C8  UNL     1       3.919   1.039  -0.228  1.00  0.00           C  
HETATM   13  O3  UNL     1       4.693   0.680  -1.145  1.00  0.00           O  
HETATM   14  O4  UNL     1       3.639   2.384  -0.049  1.00  0.00           O  
HETATM   15  H1  UNL     1       4.021  -1.252  -0.718  1.00  0.00           H  
HETATM   16  H2  UNL     1       2.924  -1.952   0.325  1.00  0.00           H  
HETATM   17  H3  UNL     1       3.668   0.220   1.692  1.00  0.00           H  
HETATM   18  H4  UNL     1       1.353  -0.525   1.281  1.00  0.00           H  
HETATM   19  H5  UNL     1       1.517   1.215   0.908  1.00  0.00           H  
HETATM   20  H6  UNL     1       1.837   0.552  -1.566  1.00  0.00           H  
HETATM   21  H7  UNL     1       1.507  -1.116  -1.065  1.00  0.00           H  
HETATM   22  H8  UNL     1      -0.972  -0.965   1.113  1.00  0.00           H  
HETATM   23  H9  UNL     1      -0.926  -2.140  -0.222  1.00  0.00           H  
HETATM   24  H10 UNL     1      -3.169  -1.204  -1.014  1.00  0.00           H  
HETATM   25  H11 UNL     1      -3.207  -1.833   0.657  1.00  0.00           H  
HETATM   26  H12 UNL     1      -2.866   1.119  -0.056  1.00  0.00           H  
HETATM   27  H13 UNL     1      -2.939   0.441   1.604  1.00  0.00           H  
HETATM   28  H14 UNL     1      -5.029   2.350   0.675  1.00  0.00           H  
HETATM   29  H15 UNL     1       3.260   2.689   0.831  1.00  0.00           H  
CONECT    1    2   15   16
CONECT    2    3   12   17
CONECT    3    4   18   19
CONECT    4    5   20   21
CONECT    5    6
CONECT    6    7   22   23
CONECT    7    8   24   25
CONECT    8    9   26   27
CONECT    9   10   10   11
CONECT   11   28
CONECT   12   13   13   14
CONECT   14   29
END

HMDB0246764
     RDKit          3D
5-(delta-Carboxybutyl)homocysteine
 29 28  0  0  0  0  0  0  0  0999 V2000
    3.7381   -1.2883    0.2919 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3050    0.0241    0.6634 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8077    0.1985    0.5733 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2973   -0.0361   -0.8269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4984    0.1735   -0.9276 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2789   -1.1429    0.0486 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7881   -1.0343    0.0116 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2653    0.2882    0.5705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7461    0.3160    0.5000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4010   -0.6542    0.0327 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4005    1.4532    0.9685 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9194    1.0387   -0.2284 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6927    0.6802   -1.1455 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6393    2.3839   -0.0490 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0215   -1.2517   -0.7181 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9240   -1.9521    0.3248 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6683    0.2204    1.6921 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3527   -0.5247    1.2806 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5173    1.2145    0.9083 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8372    0.5517   -1.5657 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5067   -1.1162   -1.0653 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9723   -0.9652    1.1132 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9261   -2.1397   -0.2215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1689   -1.2037   -1.0144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2068   -1.8330    0.6566 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8661    1.1187   -0.0557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9394    0.4413    1.6043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0292    2.3501    0.6748 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2601    2.6891    0.8306 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  2  0
  9 11  1  0
  2 12  1  0
 12 13  2  0
 12 14  1  0
  1 15  1  0
  1 16  1  0
  2 17  1  0
  3 18  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
  8 26  1  0
  8 27  1  0
 11 28  1  0
 14 29  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
5-(Δ-carboxybutyl)homocysteine	Generator
S-(alpha-Carboxybutyl)-DL-homocysteine	HMDB

Chemical Formula

C₈H₁₅NO₄S

Average Molecular Weight

221.27

Monoisotopic Molecular Weight

221.072179141

IUPAC Name

2-amino-4-[(3-carboxypropyl)sulfanyl]butanoic acid

Traditional Name

2-amino-4-[(3-carboxypropyl)sulfanyl]butanoic acid

CAS Registry Number

Not Available

SMILES

NC(CCSCCCC(O)=O)C(O)=O

InChI Identifier

InChI=1S/C8H15NO4S/c9-6(8(12)13)3-5-14-4-1-2-7(10)11/h6H,1-5,9H2,(H,10,11)(H,12,13)

InChI Key

GAWAENRCVHPTKZ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids

Alternative Parents

Substituents

Alpha-amino acid
Thia fatty acid
Dicarboxylic acid or derivatives
Fatty acid
Fatty acyl
Amino acid
Carboxylic acid
Thioether
Sulfenyl compound
Dialkylthioether
Organic oxygen compound
Primary amine
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Organic oxide
Amine
Hydrocarbon derivative
Carbonyl group
Organic nitrogen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-2.3	ALOGPS
logP	-2.3	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	2.07	ChemAxon
pKa (Strongest Basic)	9.5	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	100.62 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	53.17 m³·mol⁻¹	ChemAxon
Polarizability	23.09 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	143.368	30932474
DeepCCS	[M-H]-	139.348	30932474
DeepCCS	[M-2H]-	177.233	30932474
DeepCCS	[M+Na]+	152.81	30932474

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
5-(delta-Carboxybutyl)homocysteine	NC(CCSCCCC(O)=O)C(O)=O	3170.7	Standard polar	33892256
5-(delta-Carboxybutyl)homocysteine	NC(CCSCCCC(O)=O)C(O)=O	1788.4	Standard non polar	33892256
5-(delta-Carboxybutyl)homocysteine	NC(CCSCCCC(O)=O)C(O)=O	2162.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
5-(delta-Carboxybutyl)homocysteine,3TMS,isomer #1	C[Si](C)(C)NC(CCSCCCC(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C	2172.0	Semi standard non polar	33892256
5-(delta-Carboxybutyl)homocysteine,3TMS,isomer #1	C[Si](C)(C)NC(CCSCCCC(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C	2150.2	Standard non polar	33892256
5-(delta-Carboxybutyl)homocysteine,3TMS,isomer #1	C[Si](C)(C)NC(CCSCCCC(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C	2395.7	Standard polar	33892256
5-(delta-Carboxybutyl)homocysteine,3TMS,isomer #2	C[Si](C)(C)OC(=O)CCCSCCC(C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	2290.8	Semi standard non polar	33892256
5-(delta-Carboxybutyl)homocysteine,3TMS,isomer #2	C[Si](C)(C)OC(=O)CCCSCCC(C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	2208.4	Standard non polar	33892256
5-(delta-Carboxybutyl)homocysteine,3TMS,isomer #2	C[Si](C)(C)OC(=O)CCCSCCC(C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	2597.0	Standard polar	33892256
5-(delta-Carboxybutyl)homocysteine,3TMS,isomer #3	C[Si](C)(C)OC(=O)C(CCSCCCC(=O)O)N([Si](C)(C)C)[Si](C)(C)C	2310.9	Semi standard non polar	33892256
5-(delta-Carboxybutyl)homocysteine,3TMS,isomer #3	C[Si](C)(C)OC(=O)C(CCSCCCC(=O)O)N([Si](C)(C)C)[Si](C)(C)C	2185.5	Standard non polar	33892256
5-(delta-Carboxybutyl)homocysteine,3TMS,isomer #3	C[Si](C)(C)OC(=O)C(CCSCCCC(=O)O)N([Si](C)(C)C)[Si](C)(C)C	2572.2	Standard polar	33892256
5-(delta-Carboxybutyl)homocysteine,4TMS,isomer #1	C[Si](C)(C)OC(=O)CCCSCCC(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	2310.1	Semi standard non polar	33892256
5-(delta-Carboxybutyl)homocysteine,4TMS,isomer #1	C[Si](C)(C)OC(=O)CCCSCCC(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	2263.5	Standard non polar	33892256
5-(delta-Carboxybutyl)homocysteine,4TMS,isomer #1	C[Si](C)(C)OC(=O)CCCSCCC(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	2288.0	Standard polar	33892256
5-(delta-Carboxybutyl)homocysteine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC(CCSCCCC(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	2849.6	Semi standard non polar	33892256
5-(delta-Carboxybutyl)homocysteine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC(CCSCCCC(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	2728.6	Standard non polar	33892256
5-(delta-Carboxybutyl)homocysteine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC(CCSCCCC(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	2710.3	Standard polar	33892256
5-(delta-Carboxybutyl)homocysteine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)CCCSCCC(C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2972.6	Semi standard non polar	33892256
5-(delta-Carboxybutyl)homocysteine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)CCCSCCC(C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2764.1	Standard non polar	33892256
5-(delta-Carboxybutyl)homocysteine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)CCCSCCC(C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2813.2	Standard polar	33892256
5-(delta-Carboxybutyl)homocysteine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)C(CCSCCCC(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2982.4	Semi standard non polar	33892256
5-(delta-Carboxybutyl)homocysteine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)C(CCSCCCC(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2751.3	Standard non polar	33892256
5-(delta-Carboxybutyl)homocysteine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)C(CCSCCCC(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2804.7	Standard polar	33892256
5-(delta-Carboxybutyl)homocysteine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CCCSCCC(C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	3203.8	Semi standard non polar	33892256
5-(delta-Carboxybutyl)homocysteine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CCCSCCC(C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2980.5	Standard non polar	33892256
5-(delta-Carboxybutyl)homocysteine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CCCSCCC(C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2708.2	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (Non-derivatized) - 70eV, Positive	splash10-009f-9300000000-9a8e170cde019b0474bc	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 5-(delta-Carboxybutyl)homocysteine GC-MS (TBDMS_2_4) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-(delta-Carboxybutyl)homocysteine 10V, Positive-QTOF	splash10-0fk9-2490000000-eb0f0634284ac231cdfc	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-(delta-Carboxybutyl)homocysteine 20V, Positive-QTOF	splash10-052r-9200000000-b6c8484f179243b403b0	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-(delta-Carboxybutyl)homocysteine 40V, Positive-QTOF	splash10-052u-9000000000-5752504976ab0251f792	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-(delta-Carboxybutyl)homocysteine 10V, Negative-QTOF	splash10-01b9-0940000000-6e6ed0d4f8111841ca33	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-(delta-Carboxybutyl)homocysteine 20V, Negative-QTOF	splash10-0uxr-0900000000-d03333e6ad4e06e62582	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 5-(delta-Carboxybutyl)homocysteine 40V, Negative-QTOF	splash10-0f89-9300000000-1b6ea354a4b5d5825d1f	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

23272411

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44413151

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for 5-(delta-Carboxybutyl)homocysteine (HMDB0246764)

MOL for HMDB0246764 (5-(delta-Carboxybutyl)homocysteine)

3D MOL for HMDB0246764 (5-(delta-Carboxybutyl)homocysteine)

3D SDF for HMDB0246764 (5-(delta-Carboxybutyl)homocysteine)

3D-SDF for HMDB0246764 (5-(delta-Carboxybutyl)homocysteine)

PDB for HMDB0246764 (5-(delta-Carboxybutyl)homocysteine)

3D PDB for HMDB0246764 (5-(delta-Carboxybutyl)homocysteine)

SMILES for HMDB0246764 (5-(delta-Carboxybutyl)homocysteine)

INCHI for HMDB0246764 (5-(delta-Carboxybutyl)homocysteine)

Structure for HMDB0246764 (5-(delta-Carboxybutyl)homocysteine)

3D Structure for HMDB0246764 (5-(delta-Carboxybutyl)homocysteine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra