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Showing metabocard for (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate (HMDB0303976)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 06:07:58 UTC
Update Date2021-09-24 06:07:58 UTC
HMDB IDHMDB0303976
Secondary Accession NumbersNone
Metabolite Identification
Common Name(4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate
Description(4s)-4-hydroxy-2,3,4,5-tetrahydro-(2s)-dipicolinate belongs to alpha amino acids and derivatives class of compounds. Those 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 (4s)-4-hydroxy-2,3,4,5-tetrahydro-(2s)-dipicolinate is soluble (in water) and a weakly acidic compound (based on its pKa). (4s)-4-hydroxy-2,3,4,5-tetrahydro-(2s)-dipicolinate can be found in a number of food items such as mamey sapote, red bell pepper, burbot, and kelp, which makes (4s)-4-hydroxy-2,3,4,5-tetrahydro-(2s)-dipicolinate a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0303976 ((4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate)

  Mrv1533007131514022D          

 15 15  0  0  1  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  4  6  1  1  0  0  0
  7  5  1  0  0  0  0
  8  4  1  0  0  0  0
  8  5  2  0  0  0  0
  3  9  1  1  0  0  0
 10  6  2  0  0  0  0
 11  6  1  0  0  0  0
 12  7  1  0  0  0  0
 13  7  2  0  0  0  0
  3 14  1  6  0  0  0
  4 15  1  6  0  0  0
M  CHG  2  11  -1  12  -1
M  END
Download

3D MOL for HMDB0303976 ((4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate)

HMDB0303976
     RDKit          3D
(4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate
 20 20  0  0  0  0  0  0  0  0999 V2000
   -2.7033    2.4939    0.1738 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4460    2.4598    0.1614 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7649    3.6673    0.1264 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.7231    1.1799    0.1834 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5412    1.1967    0.1697 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3938    0.0429    0.1876 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6548    0.3252   -0.5023 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5105    1.0260    0.0938 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9789   -0.1253   -1.7723 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.6397   -1.1171   -0.4109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6135   -1.2483    0.4695 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2239   -2.4617    0.3103 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4883   -0.0729    0.2191 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6165   -0.2477    1.2398 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3294   -0.9403   -1.4542 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2255   -2.0607   -0.3789 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2209   -1.2022    1.5230 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4366   -2.6561   -0.6479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2361   -0.0229    1.0518 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0337   -0.2366   -0.7433 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
 11 13  1  0
 13  4  1  0
  6 14  1  1
 10 15  1  0
 10 16  1  0
 11 17  1  1
 12 18  1  0
 13 19  1  0
 13 20  1  0
M  CHG  2   3  -1   9  -1
M  END
Download

3D SDF for HMDB0303976 ((4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate)

  Mrv1533007131514022D          

 15 15  0  0  1  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  4  6  1  1  0  0  0
  7  5  1  0  0  0  0
  8  4  1  0  0  0  0
  8  5  2  0  0  0  0
  3  9  1  1  0  0  0
 10  6  2  0  0  0  0
 11  6  1  0  0  0  0
 12  7  1  0  0  0  0
 13  7  2  0  0  0  0
  3 14  1  6  0  0  0
  4 15  1  6  0  0  0
M  CHG  2  11  -1  12  -1
M  END
> <DATABASE_ID>
HMDB0303976

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@]1(O)CC(=N[C@@]([H])(C1)C([O-])=O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H9NO5/c9-3-1-4(6(10)11)8-5(2-3)7(12)13/h3-4,9H,1-2H2,(H,10,11)(H,12,13)/p-2/t3-,4-/m0/s1

> <INCHI_KEY>
DVTPRYHENFBCII-IMJSIDKUSA-L

> <FORMULA>
C7H7NO5

> <MOLECULAR_WEIGHT>
185.136

> <EXACT_MASS>
185.033519489

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
15.740900233524593

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate

> <ALOGPS_LOGP>
-0.90

> <JCHEM_LOGP>
-0.6398823156666666

> <ALOGPS_LOGS>
-1.04

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.866267430086415

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1319547579253704

> <JCHEM_PKA_STRONGEST_BASIC>
-2.264871455221128

> <JCHEM_POLAR_SURFACE_AREA>
112.85

> <JCHEM_REFRACTIVITY>
61.4158

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.04e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0303976 ((4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate)

HMDB0303976
     RDKit          3D
(4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate
 20 20  0  0  0  0  0  0  0  0999 V2000
   -2.7033    2.4939    0.1738 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4460    2.4598    0.1614 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7649    3.6673    0.1264 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.7231    1.1799    0.1834 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5412    1.1967    0.1697 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3938    0.0429    0.1876 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6548    0.3252   -0.5023 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5105    1.0260    0.0938 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9789   -0.1253   -1.7723 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.6397   -1.1171   -0.4109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6135   -1.2483    0.4695 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2239   -2.4617    0.3103 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4883   -0.0729    0.2191 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6165   -0.2477    1.2398 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3294   -0.9403   -1.4542 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2255   -2.0607   -0.3789 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2209   -1.2022    1.5230 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4366   -2.6561   -0.6479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2361   -0.0229    1.0518 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0337   -0.2366   -0.7433 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
 11 13  1  0
 13  4  1  0
  6 14  1  1
 10 15  1  0
 10 16  1  0
 11 17  1  1
 12 18  1  0
 13 19  1  0
 13 20  1  0
M  CHG  2   3  -1   9  -1
M  END
Download

PDB for HMDB0303976 ((4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate)

HEADER    PROTEIN                                 13-JUL-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-JUL-15         0                                  
HETATM    1  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       1.334  -0.770   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       5.335  -0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O-1
HETATM   12  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O-1
HETATM   13  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
HETATM   14  H   UNK     0       0.000   3.080   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       2.667  -1.540   0.000  0.00  0.00           H+0
CONECT    1    3    4                                                       
CONECT    2    3    5                                                       
CONECT    3    1    2    9   14                                             
CONECT    4    1    6    8   15                                             
CONECT    5    2    7    8                                                  
CONECT    6    4   10   11                                                  
CONECT    7    5   12   13                                                  
CONECT    8    4    5                                                       
CONECT    9    3                                                            
CONECT   10    6                                                            
CONECT   11    6                                                            
CONECT   12    7                                                            
CONECT   13    7                                                            
CONECT   14    3                                                            
CONECT   15    4                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END
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3D PDB for HMDB0303976 ((4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate)

COMPND    HMDB0303976
HETATM    1  O1  UNL     1      -2.703   2.494   0.174  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.446   2.460   0.161  1.00  0.00           C  
HETATM    3  O2  UNL     1      -0.765   3.667   0.126  1.00  0.00           O1-
HETATM    4  C2  UNL     1      -0.723   1.180   0.183  1.00  0.00           C  
HETATM    5  N1  UNL     1       0.541   1.197   0.170  1.00  0.00           N  
HETATM    6  C3  UNL     1       1.394   0.043   0.188  1.00  0.00           C  
HETATM    7  C4  UNL     1       2.655   0.325  -0.502  1.00  0.00           C  
HETATM    8  O3  UNL     1       3.511   1.026   0.094  1.00  0.00           O  
HETATM    9  O4  UNL     1       2.979  -0.125  -1.772  1.00  0.00           O1-
HETATM   10  C5  UNL     1       0.640  -1.117  -0.411  1.00  0.00           C  
HETATM   11  C6  UNL     1      -0.614  -1.248   0.469  1.00  0.00           C  
HETATM   12  O5  UNL     1      -1.224  -2.462   0.310  1.00  0.00           O  
HETATM   13  C7  UNL     1      -1.488  -0.073   0.219  1.00  0.00           C  
HETATM   14  H1  UNL     1       1.616  -0.248   1.240  1.00  0.00           H  
HETATM   15  H2  UNL     1       0.329  -0.940  -1.454  1.00  0.00           H  
HETATM   16  H3  UNL     1       1.225  -2.061  -0.379  1.00  0.00           H  
HETATM   17  H4  UNL     1      -0.221  -1.202   1.523  1.00  0.00           H  
HETATM   18  H5  UNL     1      -1.437  -2.656  -0.648  1.00  0.00           H  
HETATM   19  H6  UNL     1      -2.236  -0.023   1.052  1.00  0.00           H  
HETATM   20  H7  UNL     1      -2.034  -0.237  -0.743  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    4    5    5   13
CONECT    5    6
CONECT    6    7   10   14
CONECT    7    8    8    9
CONECT   10   11   15   16
CONECT   11   12   13   17
CONECT   12   18
CONECT   13   19   20
END
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SMILES for HMDB0303976 ((4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate)

[H][C@@]1(O)CC(=N[C@@]([H])(C1)C([O-])=O)C([O-])=O
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INCHI for HMDB0303976 ((4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate)

InChI=1S/C7H9NO5/c9-3-1-4(6(10)11)8-5(2-3)7(12)13/h3-4,9H,1-2H2,(H,10,11)(H,12,13)/p-2/t3-,4-/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(2S,4S)-4-Hydroxy-2,3,4,5-tetrahydrodipicolinateChEBI
(4S)-4-Hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate(2-)ChEBI
(2S,4S)-4-Hydroxy-2,3,4,5-tetrahydrodipicolinic acidGenerator
(4S)-4-Hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid(2-)Generator
(2S,4S)-4-Hydroxy-2,3,4,5-tetrahydrodipicolinic acid(2-)Generator
(4S)-4-Hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinateChEBI
(4S)-4-Hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acidGenerator
Chemical FormulaC7H7NO5
Average Molecular Weight185.136
Monoisotopic Molecular Weight185.033519489
IUPAC Name(2S,4S)-4-hydroxy-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
Traditional Name(2S,4S)-4-hydroxy-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
CAS Registry NumberNot Available
SMILES
[H][C@@]1(O)CC(=N[C@@]([H])(C1)C([O-])=O)C([O-])=O
InChI Identifier
InChI=1S/C7H9NO5/c9-3-1-4(6(10)11)8-5(2-3)7(12)13/h3-4,9H,1-2H2,(H,10,11)(H,12,13)/p-2/t3-,4-/m0/s1
InChI KeyDVTPRYHENFBCII-IMJSIDKUSA-L
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
  • Tetrahydropyridine
  • Dicarboxylic acid or derivatives
  • Hydropyridine
  • Ketimine
  • Secondary alcohol
  • Carboxylic acid
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Imine
  • Organopnictogen compound
  • Organic oxygen compound
  • Alcohol
  • Carbonyl group
  • Organic nitrogen compound
  • Organic anion
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
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 LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030124
KNApSAcK IDNot Available
Chemspider ID28533132
KEGG Compound IDNot Available
BioCyc IDCPD-14443
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound70678847
PDB IDNot Available
ChEBI ID67139
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 ReferencesNot Available