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Showing metabocard for Cystathionine ketimine (HMDB0002015)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:32 UTC
Update Date2023-02-21 17:16:03 UTC
HMDB IDHMDB0002015
Secondary Accession Numbers
  • HMDB02015
Metabolite Identification
Common NameCystathionine ketimine
DescriptionCystathionine ketimine (CT) is a cyclic amino acid that was found to have a priming effect on superoxide generation in human neutrophils (PMID: 10708546 ). D-Cystathionine ketimine and L-cystathionine ketimine enhance superoxide generation by human neutrophils in two different manners. D-Cystathionine ketimine enhanced seryl phosphorylation of 16.5-kDa protein in human neutrophils, while L-cystathionine ketimine enhanced tyrosyl phosphorylation of 45-kDa protein (PMID: 10049498 ). Cystathionine ketimine was found in the urine of a cystathioninuria patient (PMID: 8373176 ).
Structure
Data?1676999763
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0002015 (Cystathionine ketimine)

  Mrv0541 02231219192D          

 13 13  0  0  1  0            999 V2000
   17.9424   -3.4365    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   15.3736   -5.0988    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.6862   -5.0988    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.2646   -6.2159    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.7953   -6.2159    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.5299   -5.2437    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.7865   -4.8858    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.1174   -3.4365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6031   -4.0816    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.4568   -4.0816    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1415   -5.4002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9182   -5.4002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.2732   -4.8858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  1 10  1  0  0  0  0
  2 11  1  0  0  0  0
  3 12  1  0  0  0  0
  4 11  2  0  0  0  0
  5 12  2  0  0  0  0
  6  7  1  0  0  0  0
  6 13  2  0  0  0  0
  7  9  1  0  0  0  0
  7 11  1  1  0  0  0
  8  9  1  0  0  0  0
 10 13  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
Download

3D MOL for HMDB0002015 (Cystathionine ketimine)

HMDB0002015
     RDKit          3D
Cystathionine ketimine
 22 22  0  0  0  0  0  0  0  0999 V2000
    3.2053   -0.0580   -1.9203 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4168    0.5939   -1.1928 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6305    1.9546   -0.9701 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2967   -0.1098   -0.6044 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4897    0.5377    0.1348 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6551    0.3846    0.8909 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2423    1.7306    1.1436 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2963    1.8955    1.8104 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6316    2.8657    0.6406 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7615   -0.4772    0.4226 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4336   -1.9231    0.2522 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5019   -2.0523   -1.3162 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.1644   -1.5221   -0.8978 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9741    2.2776   -0.0703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3632    0.0088    1.9197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6578    3.0902   -0.3508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5938   -0.4075    1.1552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1508   -0.0869   -0.5369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3905   -2.4873    0.1878 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8579   -2.3171    1.1033 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5394   -2.1295   -0.0353 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8193   -1.7682   -1.7660 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  6 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13  4  1  0
  3 14  1  0
  6 15  1  1
  9 16  1  0
 10 17  1  0
 10 18  1  0
 11 19  1  0
 11 20  1  0
 13 21  1  0
 13 22  1  0
M  END
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3D SDF for HMDB0002015 (Cystathionine ketimine)

  Mrv0541 02231219192D          

 13 13  0  0  1  0            999 V2000
   17.9424   -3.4365    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   15.3736   -5.0988    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.6862   -5.0988    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.2646   -6.2159    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.7953   -6.2159    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.5299   -5.2437    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.7865   -4.8858    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.1174   -3.4365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6031   -4.0816    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.4568   -4.0816    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1415   -5.4002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9182   -5.4002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.2732   -4.8858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  1 10  1  0  0  0  0
  2 11  1  0  0  0  0
  3 12  1  0  0  0  0
  4 11  2  0  0  0  0
  5 12  2  0  0  0  0
  6  7  1  0  0  0  0
  6 13  2  0  0  0  0
  7  9  1  0  0  0  0
  7 11  1  1  0  0  0
  8  9  1  0  0  0  0
 10 13  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0002015

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)[C@H]1CCSCC(=N1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H9NO4S/c9-6(10)4-1-2-13-3-5(8-4)7(11)12/h4H,1-3H2,(H,9,10)(H,11,12)/t4-/m1/s1

> <INCHI_KEY>
XJUQJVUYGRTQGI-SCSAIBSYSA-N

> <FORMULA>
C7H9NO4S

> <MOLECULAR_WEIGHT>
203.216

> <EXACT_MASS>
203.025228471

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
18.442346082610634

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(5R)-2,5,6,7-tetrahydro-1,4-thiazepine-3,5-dicarboxylic acid

> <ALOGPS_LOGP>
-0.09

> <JCHEM_LOGP>
0.3903825910000002

> <ALOGPS_LOGS>
-1.63

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.9664414229319367

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2398428110676822

> <JCHEM_PKA_STRONGEST_BASIC>
-2.2790816811427703

> <JCHEM_POLAR_SURFACE_AREA>
86.96

> <JCHEM_REFRACTIVITY>
46.199200000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.81e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cystathionine ketimine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0002015 (Cystathionine ketimine)

HMDB0002015
     RDKit          3D
Cystathionine ketimine
 22 22  0  0  0  0  0  0  0  0999 V2000
    3.2053   -0.0580   -1.9203 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4168    0.5939   -1.1928 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6305    1.9546   -0.9701 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2967   -0.1098   -0.6044 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4897    0.5377    0.1348 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6551    0.3846    0.8909 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2423    1.7306    1.1436 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2963    1.8955    1.8104 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6316    2.8657    0.6406 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7615   -0.4772    0.4226 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4336   -1.9231    0.2522 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5019   -2.0523   -1.3162 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.1644   -1.5221   -0.8978 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9741    2.2776   -0.0703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3632    0.0088    1.9197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6578    3.0902   -0.3508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5938   -0.4075    1.1552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1508   -0.0869   -0.5369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3905   -2.4873    0.1878 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8579   -2.3171    1.1033 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5394   -2.1295   -0.0353 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8193   -1.7682   -1.7660 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  6 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13  4  1  0
  3 14  1  0
  6 15  1  1
  9 16  1  0
 10 17  1  0
 10 18  1  0
 11 19  1  0
 11 20  1  0
 13 21  1  0
 13 22  1  0
M  END
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PDB for HMDB0002015 (Cystathionine ketimine)

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  S   UNK     0      33.492  -6.415   0.000  0.00  0.00           S+0
HETATM    2  O   UNK     0      28.697  -9.518   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      36.748  -9.518   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      30.361 -11.603   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      35.085 -11.603   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0      32.722  -9.788   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      31.335  -9.120   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      31.952  -6.415   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      30.992  -7.619   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      34.453  -7.619   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      30.131 -10.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      35.314 -10.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      34.110  -9.120   0.000  0.00  0.00           C+0
CONECT    1    8   10                                                       
CONECT    2   11                                                            
CONECT    3   12                                                            
CONECT    4   11                                                            
CONECT    5   12                                                            
CONECT    6    7   13                                                       
CONECT    7    6    9   11                                                  
CONECT    8    1    9                                                       
CONECT    9    7    8                                                       
CONECT   10    1   13                                                       
CONECT   11    2    4    7                                                  
CONECT   12    3    5   13                                                  
CONECT   13    6   10   12                                                  
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END
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3D PDB for HMDB0002015 (Cystathionine ketimine)

COMPND    HMDB0002015
HETATM    1  O1  UNL     1       3.205  -0.058  -1.920  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.417   0.594  -1.193  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.630   1.955  -0.970  1.00  0.00           O  
HETATM    4  C2  UNL     1       1.297  -0.110  -0.604  1.00  0.00           C  
HETATM    5  N1  UNL     1       0.490   0.538   0.135  1.00  0.00           N  
HETATM    6  C3  UNL     1      -0.655   0.385   0.891  1.00  0.00           C  
HETATM    7  C4  UNL     1      -1.242   1.731   1.144  1.00  0.00           C  
HETATM    8  O3  UNL     1      -2.296   1.896   1.810  1.00  0.00           O  
HETATM    9  O4  UNL     1      -0.632   2.866   0.641  1.00  0.00           O  
HETATM   10  C5  UNL     1      -1.761  -0.477   0.423  1.00  0.00           C  
HETATM   11  C6  UNL     1      -1.434  -1.923   0.252  1.00  0.00           C  
HETATM   12  S1  UNL     1      -0.502  -2.052  -1.316  1.00  0.00           S  
HETATM   13  C7  UNL     1       1.164  -1.522  -0.898  1.00  0.00           C  
HETATM   14  H1  UNL     1       2.974   2.278  -0.070  1.00  0.00           H  
HETATM   15  H2  UNL     1      -0.363   0.009   1.920  1.00  0.00           H  
HETATM   16  H3  UNL     1      -0.658   3.090  -0.351  1.00  0.00           H  
HETATM   17  H4  UNL     1      -2.594  -0.407   1.155  1.00  0.00           H  
HETATM   18  H5  UNL     1      -2.151  -0.087  -0.537  1.00  0.00           H  
HETATM   19  H6  UNL     1      -2.390  -2.487   0.188  1.00  0.00           H  
HETATM   20  H7  UNL     1      -0.858  -2.317   1.103  1.00  0.00           H  
HETATM   21  H8  UNL     1       1.539  -2.130  -0.035  1.00  0.00           H  
HETATM   22  H9  UNL     1       1.819  -1.768  -1.766  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   14
CONECT    4    5    5   13
CONECT    5    6
CONECT    6    7   10   15
CONECT    7    8    8    9
CONECT    9   16
CONECT   10   11   17   18
CONECT   11   12   19   20
CONECT   12   13
CONECT   13   21   22
END
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SMILES for HMDB0002015 (Cystathionine ketimine)

OC(=O)[C@H]1CCSCC(=N1)C(O)=O
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INCHI for HMDB0002015 (Cystathionine ketimine)

InChI=1S/C7H9NO4S/c9-6(10)4-1-2-13-3-5(8-4)7(11)12/h4H,1-3H2,(H,9,10)(H,11,12)/t4-/m1/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(5R)-1-Thia-4-azacyclohepta-3-ene-3,5-dicarboxylic acidChEBI
(R)-2,5,6,7-Tetrahydro-1,4-thiazepine-3,5-dicarboxylic acidChEBI
(5R)-1-Thia-4-azacyclohepta-3-ene-3,5-dicarboxylateGenerator
(R)-2,5,6,7-Tetrahydro-1,4-thiazepine-3,5-dicarboxylateGenerator
(5R)-2,5,6,7-tetrahydro-1,4-Thiazepine-3,5-dicarboxylic acidHMDB
(5R)-2,5,6,7-Tetrahydro-1,4-thiazepine-3,5-dicarboxylateGenerator, HMDB
Cystathionine ketimineMeSH
CTHMDB
Chemical FormulaC7H9NO4S
Average Molecular Weight203.216
Monoisotopic Molecular Weight203.025228471
IUPAC Name(5R)-2,5,6,7-tetrahydro-1,4-thiazepine-3,5-dicarboxylic acid
Traditional Namecystathionine ketimine
CAS Registry Number87254-95-3
SMILES
OC(=O)[C@H]1CCSCC(=N1)C(O)=O
InChI Identifier
InChI=1S/C7H9NO4S/c9-6(10)4-1-2-13-3-5(8-4)7(11)12/h4H,1-3H2,(H,9,10)(H,11,12)/t4-/m1/s1
InChI KeyXJUQJVUYGRTQGI-SCSAIBSYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids and derivatives
Alternative Parents
Substituents
  • Alpha-amino acid or derivatives
  • Dicarboxylic acid or derivatives
  • Ketimine
  • Carboxylic acid
  • Thioether
  • Azacycle
  • Organoheterocyclic compound
  • Dialkylthioether
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Imine
  • Organopnictogen compound
  • Organic oxygen compound
  • Carbonyl group
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
 details
UrineDetected and Quantified0.33 umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected and Quantified408.147 umol/mmol creatinineNot SpecifiedNot SpecifiedCystathioninuria details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022797
KNApSAcK IDNot Available
Chemspider ID119692
KEGG Compound IDNot Available
BioCyc IDCPD-16729
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID6438
PubChem Compound135905
PDB IDNot Available
ChEBI ID90001
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Okada T, Takechi T, Wakiguchi H, Kurashige T, Sugahara K, Kodama H: Identification of new cystathionine mono-oxo acids, S-(3-oxo-3-carboxy-n-propyl) cysteine and S-(2-oxo-2-carboxyethyl) homocysteine, in the urine of a patient with cystathioninuria. Arch Biochem Biophys. 1993 Sep;305(2):385-91. [PubMed:8373176 ]
  2. Pecci L, Antonucci A, Nardini M, Cavallini D: Detection of cystathionine and lanthionine ketimines in human urine. Biochem Int. 1988 Nov;17(5):877-83. [PubMed:3254164 ]
  3. Antonucci A, Pecci L, Fontana M, Cavallini D: Influence of diet on cystathionine ketimine and lanthionine ketimine content in human urine. Ital J Biochem. 1990 Mar-Apr;39(2):100-5. [PubMed:2361849 ]
  4. Zhang J, Zhang M, Sugahara K, Sagara Y, Spirito A, Dupre, Kodama H: D-cystathionine ketimine and L-cystathionine ketimine enhance superoxide generation by human neutrophils in a different manner. Arch Biochem Biophys. 1999 Mar 1;363(1):55-9. [PubMed:10049498 ]
  5. Kodama H, Zhang J, Sugahara K: Novel priming compounds of cystathionine metabolites on superoxide generation in human neutrophils. Biochem Biophys Res Commun. 2000 Mar 16;269(2):297-301. [PubMed:10708546 ]