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Showing metabocard for Tetrahydrodipicolinate (HMDB0012289)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2009-04-06 16:22:24 UTC
Update Date2023-02-21 17:17:48 UTC
HMDB IDHMDB0012289
Secondary Accession Numbers
  • HMDB12289
Metabolite Identification
Common NameTetrahydrodipicolinate
DescriptionTetrahydrodipicolinate (CAS: 2353-17-5), converted from L-aspartate, is an important intermediate in the lysine biosynthesis pathway. Several pathways are now recognized in bacteria, most algae, fungi, and higher plants for the biosynthesis of lysine. They are divided into two groups: (1) the diaminopimelate (DAP) pathways, and (2) the alpha-aminoadipate (AAA) pathways. In the pathways that belong to the DAP group, lysine is produced from aspartate (along with methionine, threonine, and isoleucine). All of these pathways share the upper segments, which include the four steps required for the conversion of L-aspartate into tetrahydrodipicolinate. They also share the last step, which is the conversion of the intermediate meso-diaminopimelate (D,L-DAP, or meso-DAP) into lysine. However, these pathways differ in the routes leading from tetrahydrodipicolinate to meso-diaminopimelate. The four variations include: (I) the succinylase variant, which involves succinylated intermediates, where tetrahydrodipicolinate is converted into meso-diaminopimelate in four enzymatic steps; (II) the acetylase variant, which involves acetylated intermediates, where tetrahydrodipicolinate is converted into meso-diaminopimelate in four enzymatic steps; (III) the dehydrogenase variant, in which tetrahydrodipicolinate is converted into meso-diaminopimelate in a single enzymatic step; and (IV) the diaminopimelate-aminotransferase variant, in which tetrahydrodipicolinate is converted into meso-diaminopimelate in two steps. In addition to lysine, the pathways in this group also produce meso-DAP, which is an important metabolite on its own.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0012289 (Tetrahydrodipicolinate)

  Mrv1652309042000362D          

 12 12  0  0  0  0            999 V2000
 9981.3441 9979.6231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9982.0575 9980.0345    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9981.3441 9978.7985    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9980.6289 9980.0345    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9980.6289 9980.8595    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9979.9158 9979.6231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9979.9158 9981.2718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9979.1997 9980.0345    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9979.9158 9982.0963    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9979.1997 9980.8595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9979.2018 9982.5086    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9980.6289 9982.5086    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  4  1  1  6  0  0  0
  7  9  1  0  0  0  0
  9 11  1  0  0  0  0
  9 12  2  0  0  0  0
 10  7  1  0  0  0  0
  7  5  2  0  0  0  0
  5  4  1  0  0  0  0
  4  6  1  0  0  0  0
  6  8  1  0  0  0  0
  8 10  1  0  0  0  0
M  END
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3D MOL for HMDB0012289 (Tetrahydrodipicolinate)

HMDB0012289
     RDKit          3D
Tetrahydrodipicolinate
 21 21  0  0  0  0  0  0  0  0999 V2000
   -2.3972    0.5308   -2.6059 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3647    0.4702   -1.3523 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5799    0.4503   -0.6864 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1201    0.4220   -0.6082 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0273    0.4412   -1.2450 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1729    0.3857   -0.3353 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4548    0.3733   -1.0396 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6060    0.4054   -2.2853 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6046    0.3214   -0.2618 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9343   -0.8974    0.4698 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1215   -0.5274    1.4880 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1542    0.3539    0.8671 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9786   -0.4151   -0.3330 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1081    1.2854    0.3027 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7847   -0.5830    0.1897 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8634   -1.2732    0.9224 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5220   -1.6622   -0.2213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5448   -1.4494    1.9389 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4296    0.0366    2.2977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1575   -0.0507    1.1799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0892    1.3826    1.3176 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  4  1  0
  3 13  1  0
  6 14  1  1
  9 15  1  0
 10 16  1  0
 10 17  1  0
 11 18  1  0
 11 19  1  0
 12 20  1  0
 12 21  1  0
M  END
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3D SDF for HMDB0012289 (Tetrahydrodipicolinate)

  Mrv1652309042000362D          

 12 12  0  0  0  0            999 V2000
 9981.3441 9979.6231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9982.0575 9980.0345    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9981.3441 9978.7985    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9980.6289 9980.0345    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9980.6289 9980.8595    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9979.9158 9979.6231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9979.9158 9981.2718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9979.1997 9980.0345    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9979.9158 9982.0963    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9979.1997 9980.8595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9979.2018 9982.5086    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9980.6289 9982.5086    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  4  1  1  6  0  0  0
  7  9  1  0  0  0  0
  9 11  1  0  0  0  0
  9 12  2  0  0  0  0
 10  7  1  0  0  0  0
  7  5  2  0  0  0  0
  5  4  1  0  0  0  0
  4  6  1  0  0  0  0
  6  8  1  0  0  0  0
  8 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0012289

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H9NO4/c9-6(10)4-2-1-3-5(8-4)7(11)12/h4H,1-3H2,(H,9,10)(H,11,12)/t4-/m0/s1

> <INCHI_KEY>
CXMBCXQHOXUCEO-BYPYZUCNSA-N

> <FORMULA>
C7H9NO4

> <MOLECULAR_WEIGHT>
171.1507

> <EXACT_MASS>
171.053157781

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
15.741012521213165

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid

> <ALOGPS_LOGP>
0.18

> <JCHEM_LOGP>
0.6637227573333334

> <ALOGPS_LOGS>
-1.42

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.029293071950575

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2790735427432285

> <JCHEM_PKA_STRONGEST_BASIC>
-1.992097040181755

> <JCHEM_POLAR_SURFACE_AREA>
86.96000000000001

> <JCHEM_REFRACTIVITY>
38.2697

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.49e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0012289 (Tetrahydrodipicolinate)

HMDB0012289
     RDKit          3D
Tetrahydrodipicolinate
 21 21  0  0  0  0  0  0  0  0999 V2000
   -2.3972    0.5308   -2.6059 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3647    0.4702   -1.3523 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5799    0.4503   -0.6864 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1201    0.4220   -0.6082 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0273    0.4412   -1.2450 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1729    0.3857   -0.3353 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4548    0.3733   -1.0396 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6060    0.4054   -2.2853 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6046    0.3214   -0.2618 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9343   -0.8974    0.4698 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1215   -0.5274    1.4880 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1542    0.3539    0.8671 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9786   -0.4151   -0.3330 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1081    1.2854    0.3027 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7847   -0.5830    0.1897 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8634   -1.2732    0.9224 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5220   -1.6622   -0.2213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5448   -1.4494    1.9389 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4296    0.0366    2.2977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1575   -0.0507    1.1799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0892    1.3826    1.3176 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  4  1  0
  3 13  1  0
  6 14  1  1
  9 15  1  0
 10 16  1  0
 10 17  1  0
 11 18  1  0
 11 19  1  0
 12 20  1  0
 12 21  1  0
M  END
Download

PDB for HMDB0012289 (Tetrahydrodipicolinate)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0    8631.8428628.630   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    8633.1748629.398   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8631.8428627.091   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0    8630.5078629.398   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0    8630.5078630.938   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0    8629.1768628.630   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8629.1768631.707   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8627.8398629.398   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8629.1768633.246   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8627.8398630.938   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0    8627.8438634.016   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0    8630.5078634.016   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    5    6                                                  
CONECT    5    7    4                                                       
CONECT    6    4    8                                                       
CONECT    7    9   10    5                                                  
CONECT    8    6   10                                                       
CONECT    9    7   11   12                                                  
CONECT   10    7    8                                                       
CONECT   11    9                                                            
CONECT   12    9                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END
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3D PDB for HMDB0012289 (Tetrahydrodipicolinate)

COMPND    HMDB0012289
HETATM    1  O1  UNL     1      -2.397   0.531  -2.606  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.365   0.470  -1.352  1.00  0.00           C  
HETATM    3  O2  UNL     1      -3.580   0.450  -0.686  1.00  0.00           O  
HETATM    4  C2  UNL     1      -1.120   0.422  -0.608  1.00  0.00           C  
HETATM    5  N1  UNL     1       0.027   0.441  -1.245  1.00  0.00           N  
HETATM    6  C3  UNL     1       1.173   0.386  -0.335  1.00  0.00           C  
HETATM    7  C4  UNL     1       2.455   0.373  -1.040  1.00  0.00           C  
HETATM    8  O3  UNL     1       2.606   0.405  -2.285  1.00  0.00           O  
HETATM    9  O4  UNL     1       3.605   0.321  -0.262  1.00  0.00           O  
HETATM   10  C5  UNL     1       0.934  -0.897   0.470  1.00  0.00           C  
HETATM   11  C6  UNL     1      -0.122  -0.527   1.488  1.00  0.00           C  
HETATM   12  C7  UNL     1      -1.154   0.354   0.867  1.00  0.00           C  
HETATM   13  H1  UNL     1      -3.979  -0.415  -0.333  1.00  0.00           H  
HETATM   14  H2  UNL     1       1.108   1.285   0.303  1.00  0.00           H  
HETATM   15  H3  UNL     1       3.785  -0.583   0.190  1.00  0.00           H  
HETATM   16  H4  UNL     1       1.863  -1.273   0.922  1.00  0.00           H  
HETATM   17  H5  UNL     1       0.522  -1.662  -0.221  1.00  0.00           H  
HETATM   18  H6  UNL     1      -0.545  -1.449   1.939  1.00  0.00           H  
HETATM   19  H7  UNL     1       0.430   0.037   2.298  1.00  0.00           H  
HETATM   20  H8  UNL     1      -2.158  -0.051   1.180  1.00  0.00           H  
HETATM   21  H9  UNL     1      -1.089   1.383   1.318  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   13
CONECT    4    5    5   12
CONECT    5    6
CONECT    6    7   10   14
CONECT    7    8    8    9
CONECT    9   15
CONECT   10   11   16   17
CONECT   11   12   18   19
CONECT   12   20   21
END
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SMILES for HMDB0012289 (Tetrahydrodipicolinate)

OC(=O)[C@@H]1CCCC(=N1)C(O)=O
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INCHI for HMDB0012289 (Tetrahydrodipicolinate)

InChI=1S/C7H9NO4/c9-6(10)4-2-1-3-5(8-4)7(11)12/h4H,1-3H2,(H,9,10)(H,11,12)/t4-/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
L-2,3,4,5-Tetrahydrodipicolinic acidChEBI
Delta1-Piperidine-2,6-dicarboxylateKegg
L-2,3,4,5-TetrahydrodipicolinateKegg
(S)-2,3,4,5-Tetrahydropyridine-2,6-dicarboxylateKegg
delta1-Piperidine-2,6-dicarboxylic acidGenerator
Δ1-piperidine-2,6-dicarboxylateGenerator
Δ1-piperidine-2,6-dicarboxylic acidGenerator
(S)-2,3,4,5-Tetrahydropyridine-2,6-dicarboxylic acidGenerator
Tetrahydrodipicolinic acidGenerator
(S)-2,3,4,5-TetrahydrodipicolinateHMDB
(2S)-2,3,4,5-Tetrahydro-2,6-pyridinedicarboxylic acidHMDB
(2S)-2,3,4,5-Tetrahydropyridine-2,6-dicarboxylic acidHMDB
2,3,4,5-Tetrahydro-2,6-pyridinedicarboxylic acidHMDB
2,3,4,5-TetrahydrodipicolinateHMDB
Chemical FormulaC7H9NO4
Average Molecular Weight171.1507
Monoisotopic Molecular Weight171.053157781
IUPAC Name(2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
Traditional Name(2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylic acid
CAS Registry Number4226-22-6
SMILES
OC(=O)[C@@H]1CCCC(=N1)C(O)=O
InChI Identifier
InChI=1S/C7H9NO4/c9-6(10)4-2-1-3-5(8-4)7(11)12/h4H,1-3H2,(H,9,10)(H,11,12)/t4-/m0/s1
InChI KeyCXMBCXQHOXUCEO-BYPYZUCNSA-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
  • Tetrahydropyridine
  • Dicarboxylic acid or derivatives
  • Hydropyridine
  • Ketimine
  • Azacycle
  • Organoheterocyclic compound
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carboxylic acid
  • Hydrocarbon derivative
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Imine
  • Organic nitrogen compound
  • Carbonyl group
  • Organic oxide
  • Organopnictogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
Process
Naturally occurring process
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 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 IDNot Available
KNApSAcK IDC00007502
Chemspider ID389168
KEGG Compound IDC03972
BioCyc IDDELTA1-PIPERIDEINE-2-6-DICARBOXYLATE
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound440179
PDB IDNot Available
ChEBI ID864
Food Biomarker OntologyNot Available
VMH IDTHDP
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available