Showing metabocard for (S)-2,3,4,5-tetrahydrodipicolinate (MMDBc0032110)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-18 02:02:48 UTC
Update Date2022-08-31 18:30:37 UTC
Metabolite IDMMDBc0032110
Metabolite Identification
Common Name(S)-2,3,4,5-tetrahydrodipicolinate
Description(S)-2,3,4,5-tetrahydrodipicolinate is an intermediate in L-lysine biosynthesis I pathway in E.coli. It is a substrate for the enzyme tetrahydrodipicolinate succinylase which catalyzes the reaction (S)-2,3,4,5-tetrahydrodipicolinate + succinyl-CoA + H2O -> N-succinyl-2-amino-6-ketopimelate + coenzyme A. It is also a product for enzyme 4-hydroxy-tetrahydrodipicolinate reductase which catalyzes reaction (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NADPH + H+ -> (S)-2,3,4,5-tetrahydrodipicolinate + NADP+ + H2O (BioCyc compound: DELTA1-PIPERIDEINE-2-6-DICARBOXYLATE).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fdb70b36fe8>


  Mrv1652303082006152D          

 12 12  0  0  0  0            999 V2000
    1.4289    0.0000    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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   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   -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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
  3 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
M  CHG  2   8  -1  11  -1
M  END
Download

3D MOL for #<Metabolite:0x00007fdb70b36fe8>

HMDB0303994
     RDKit          3D
(S)-2,3,4,5-tetrahydrodipicolinate
 19 19  0  0  0  0  0  0  0  0999 V2000
    3.3013    1.2761    0.0723 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3040    1.2963    0.8392 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3253    1.9259    2.0764 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.0906    0.6338    0.4051 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0543    0.6253    1.1433 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1922   -0.0117    0.7841 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0698    1.0047    0.1448 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3055    0.7653    0.1428 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6143    2.1663   -0.4317 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.0245   -1.2115   -0.0878 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3156   -1.3622   -0.7071 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0308   -0.0430   -0.8981 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6916   -0.2861    1.7454 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2969   -2.1302    0.5088 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8086   -1.1750   -0.8965 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9987   -2.0255   -0.1405 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2187   -1.8255   -1.7197 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3754    0.5624   -1.5925 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9887   -0.1857   -1.3882 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
  6 13  1  0
 10 14  1  0
 10 15  1  0
 11 16  1  0
 11 17  1  0
 12 18  1  0
 12 19  1  0
M  CHG  2   3  -1   9  -1
M  END
Download

3D SDF for #<Metabolite:0x00007fdb70b36fe8>


  Mrv1652303082006152D          

 12 12  0  0  0  0            999 V2000
    1.4289    0.0000    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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   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   -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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
  3 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
M  CHG  2   8  -1  11  -1
M  END
> <DATABASE_ID>
MMDBc0032110

> <DATABASE_NAME>
MIME

> <SMILES>
[O-]C(=O)C1CCCC(=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)/p-2

> <INCHI_KEY>
CXMBCXQHOXUCEO-UHFFFAOYSA-L

> <FORMULA>
C7H7NO4

> <MOLECULAR_WEIGHT>
169.137

> <EXACT_MASS>
169.038604869

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
14.837957068663458

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate

> <ALOGPS_LOGP>
0.02

> <JCHEM_LOGP>
0.6637227573333334

> <ALOGPS_LOGS>
-1.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.029293071950576

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2790735427432276

> <JCHEM_PKA_STRONGEST_BASIC>
-1.992097040181755

> <JCHEM_POLAR_SURFACE_AREA>
92.62

> <JCHEM_REFRACTIVITY>
59.943900000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.42e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3,4,5-tetrahydrodipicolinate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007fdb70b36fe8>

HMDB0303994
     RDKit          3D
(S)-2,3,4,5-tetrahydrodipicolinate
 19 19  0  0  0  0  0  0  0  0999 V2000
    3.3013    1.2761    0.0723 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3040    1.2963    0.8392 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3253    1.9259    2.0764 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.0906    0.6338    0.4051 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0543    0.6253    1.1433 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1922   -0.0117    0.7841 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0698    1.0047    0.1448 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3055    0.7653    0.1428 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6143    2.1663   -0.4317 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.0245   -1.2115   -0.0878 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3156   -1.3622   -0.7071 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0308   -0.0430   -0.8981 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6916   -0.2861    1.7454 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2969   -2.1302    0.5088 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8086   -1.1750   -0.8965 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9987   -2.0255   -0.1405 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2187   -1.8255   -1.7197 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3754    0.5624   -1.5925 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9887   -0.1857   -1.3882 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
  6 13  1  0
 10 14  1  0
 10 15  1  0
 11 16  1  0
 11 17  1  0
 12 18  1  0
 12 19  1  0
M  CHG  2   3  -1   9  -1
M  END
Download

PDB for #<Metabolite:0x00007fdb70b36fe8>

HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O-1
HETATM    9  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O-1
HETATM   12  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   10                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    3   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END
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3D PDB for #<Metabolite:0x00007fdb70b36fe8>

COMPND    HMDB0303994
HETATM    1  O1  UNL     1       3.301   1.276   0.072  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.304   1.296   0.839  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.325   1.926   2.076  1.00  0.00           O1-
HETATM    4  C2  UNL     1       1.091   0.634   0.405  1.00  0.00           C  
HETATM    5  N1  UNL     1       0.054   0.625   1.143  1.00  0.00           N  
HETATM    6  C3  UNL     1      -1.192  -0.012   0.784  1.00  0.00           C  
HETATM    7  C4  UNL     1      -2.070   1.005   0.145  1.00  0.00           C  
HETATM    8  O3  UNL     1      -3.305   0.765   0.143  1.00  0.00           O  
HETATM    9  O4  UNL     1      -1.614   2.166  -0.432  1.00  0.00           O1-
HETATM   10  C5  UNL     1      -1.025  -1.211  -0.088  1.00  0.00           C  
HETATM   11  C6  UNL     1       0.316  -1.362  -0.707  1.00  0.00           C  
HETATM   12  C7  UNL     1       1.031  -0.043  -0.898  1.00  0.00           C  
HETATM   13  H1  UNL     1      -1.692  -0.286   1.745  1.00  0.00           H  
HETATM   14  H2  UNL     1      -1.297  -2.130   0.509  1.00  0.00           H  
HETATM   15  H3  UNL     1      -1.809  -1.175  -0.897  1.00  0.00           H  
HETATM   16  H4  UNL     1       0.999  -2.026  -0.141  1.00  0.00           H  
HETATM   17  H5  UNL     1       0.219  -1.825  -1.720  1.00  0.00           H  
HETATM   18  H6  UNL     1       0.375   0.562  -1.592  1.00  0.00           H  
HETATM   19  H7  UNL     1       1.989  -0.186  -1.388  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    4    5    5   12
CONECT    5    6
CONECT    6    7   10   13
CONECT    7    8    8    9
CONECT   10   11   14   15
CONECT   11   12   16   17
CONECT   12   18   19
END
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SMILES for #<Metabolite:0x00007fdb70b36fe8>

[O-]C(=O)C1CCCC(=N1)C([O-])=O
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INCHI for #<Metabolite:0x00007fdb70b36fe8>

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)/p-2
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Synonyms
ValueSource
2,3,4,5-TetrahydrodipicolinateChEBI
2,3,4,5-Tetrahydrodipicolinic acidGenerator
(S)-2,3,4,5-Tetrahydrodipicolinic acidGenerator
2,3,4,5-Tetrahydrodipicolinic acid(2-)Generator
Molecular FormulaC7H7NO4
Average Mass169.137
Monoisotopic Mass169.038604869
IUPAC Name2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
Traditional Name2,3,4,5-tetrahydrodipicolinate
CAS Registry NumberNot Available
SMILES
[O-]C(=O)C1CCCC(=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)/p-2
InChI KeyCXMBCXQHOXUCEO-UHFFFAOYSA-L