Showing metabocard for 2,3-Dihydrodipicolinic acid (MMDBc0029776)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:41:12 UTC
Update Date2022-08-31 17:16:52 UTC
Metabolite IDMMDBc0029776
Metabolite Identification
Common Name2,3-Dihydrodipicolinic acid
DescriptionL-2,3-Dihydrodipicolinate is involved in the lysine biosynthesis pathway. L-2,3-Dihydrodipicolinate is produced from a reaction between pyruvate and L-aspartate-semialdehyde, with water as a byproduct. The reaction is catalyzed by dihydrodipicolinate synthase.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f92109e46d0>


  Mrv0541 02241203522D          

 12 12  0  0  0  0            999 V2000
   15.9805  -11.6086    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5680  -12.3225    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8055  -11.6086    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.5680  -10.8939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9805  -10.1795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5680   -9.4648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7430   -9.4648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3305  -10.1795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7430  -10.8939    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.5055  -10.1795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0931   -9.4648    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.0931  -10.8939    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  9  2  0  0  0  0
  5  6  2  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
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f92109e46d0>

HMDB0012247
     RDKit          3D
L-2,3-Dihydrodipicolinate
 19 19  0  0  0  0  0  0  0  0999 V2000
   -2.8269   -1.9295   -0.2562 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6775   -0.7148   -0.0057 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7292    0.1129    0.3880 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3279   -0.1560   -0.1380 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3335   -0.8798   -0.4967 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0154   -0.4438   -0.6571 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9131   -1.3249    0.1512 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4320   -2.2700    0.8254 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2852   -1.1217    0.1755 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2741    0.9964   -0.3757 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0939    1.7630    0.0288 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0987    1.2381    0.1384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2078   -0.0926    1.2670 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2675   -0.6130   -1.7478 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8444   -1.8410   -0.2995 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0467    1.0630    0.4397 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7387    1.5327   -1.2408 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2282    2.8248    0.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9377    1.8563    0.4428 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  2  0
 12  4  1  0
  3 13  1  0
  6 14  1  0
  9 15  1  0
 10 16  1  0
 10 17  1  0
 11 18  1  0
 12 19  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f92109e46d0>


  Mrv0541 02241203522D          

 12 12  0  0  0  0            999 V2000
   15.9805  -11.6086    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5680  -12.3225    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8055  -11.6086    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.5680  -10.8939    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9805  -10.1795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5680   -9.4648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7430   -9.4648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3305  -10.1795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7430  -10.8939    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.5055  -10.1795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0931   -9.4648    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.0931  -10.8939    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  9  2  0  0  0  0
  5  6  2  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
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029776

> <DATABASE_NAME>
MIME

> <SMILES>
OC(=O)C1CC=CC(=N1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H7NO4/c9-6(10)4-2-1-3-5(8-4)7(11)12/h1-2,5H,3H2,(H,9,10)(H,11,12)

> <INCHI_KEY>
UWOCFOFVIBZJGH-UHFFFAOYSA-N

> <FORMULA>
C7H7NO4

> <MOLECULAR_WEIGHT>
169.1348

> <EXACT_MASS>
169.037507717

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
15.076256835994267

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3-dihydropyridine-2,6-dicarboxylic acid

> <ALOGPS_LOGP>
0.12

> <JCHEM_LOGP>
0.661546247

> <ALOGPS_LOGS>
-1.39

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.918452620053926

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1703299368072653

> <JCHEM_PKA_STRONGEST_BASIC>
-1.0507329103103578

> <JCHEM_POLAR_SURFACE_AREA>
86.96

> <JCHEM_REFRACTIVITY>
39.36300000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.84e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3-dihydrodipicolinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f92109e46d0>

HMDB0012247
     RDKit          3D
L-2,3-Dihydrodipicolinate
 19 19  0  0  0  0  0  0  0  0999 V2000
   -2.8269   -1.9295   -0.2562 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6775   -0.7148   -0.0057 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7292    0.1129    0.3880 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3279   -0.1560   -0.1380 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3335   -0.8798   -0.4967 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0154   -0.4438   -0.6571 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9131   -1.3249    0.1512 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4320   -2.2700    0.8254 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2852   -1.1217    0.1755 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2741    0.9964   -0.3757 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0939    1.7630    0.0288 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0987    1.2381    0.1384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2078   -0.0926    1.2670 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2675   -0.6130   -1.7478 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8444   -1.8410   -0.2995 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0467    1.0630    0.4397 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7387    1.5327   -1.2408 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2282    2.8248    0.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9377    1.8563    0.4428 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  2  0
 12  4  1  0
  3 13  1  0
  6 14  1  0
  9 15  1  0
 10 16  1  0
 10 17  1  0
 11 18  1  0
 12 19  1  0
M  END
Download

PDB for #<Metabolite:0x00007f92109e46d0>

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      29.830 -21.669   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      29.060 -23.002   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      31.370 -21.669   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      29.060 -20.335   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      29.830 -19.002   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      29.060 -17.668   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      27.520 -17.668   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      26.750 -19.002   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      27.520 -20.335   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      25.210 -19.002   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      24.440 -17.668   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      24.440 -20.335   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    4    8                                                       
CONECT   10    8   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:0x00007f92109e46d0>

COMPND    HMDB0012247
HETATM    1  O1  UNL     1      -2.827  -1.930  -0.256  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.677  -0.715  -0.006  1.00  0.00           C  
HETATM    3  O2  UNL     1      -3.729   0.113   0.388  1.00  0.00           O  
HETATM    4  C2  UNL     1      -1.328  -0.156  -0.138  1.00  0.00           C  
HETATM    5  N1  UNL     1      -0.334  -0.880  -0.497  1.00  0.00           N  
HETATM    6  C3  UNL     1       1.015  -0.444  -0.657  1.00  0.00           C  
HETATM    7  C4  UNL     1       1.913  -1.325   0.151  1.00  0.00           C  
HETATM    8  O3  UNL     1       1.432  -2.270   0.825  1.00  0.00           O  
HETATM    9  O4  UNL     1       3.285  -1.122   0.176  1.00  0.00           O  
HETATM   10  C5  UNL     1       1.274   0.996  -0.376  1.00  0.00           C  
HETATM   11  C6  UNL     1       0.094   1.763   0.029  1.00  0.00           C  
HETATM   12  C7  UNL     1      -1.099   1.238   0.138  1.00  0.00           C  
HETATM   13  H1  UNL     1      -4.208  -0.093   1.267  1.00  0.00           H  
HETATM   14  H2  UNL     1       1.268  -0.613  -1.748  1.00  0.00           H  
HETATM   15  H3  UNL     1       3.844  -1.841  -0.299  1.00  0.00           H  
HETATM   16  H4  UNL     1       2.047   1.063   0.440  1.00  0.00           H  
HETATM   17  H5  UNL     1       1.739   1.533  -1.241  1.00  0.00           H  
HETATM   18  H6  UNL     1       0.228   2.825   0.247  1.00  0.00           H  
HETATM   19  H7  UNL     1      -1.938   1.856   0.443  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   12   18
CONECT   12   19
END
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SMILES for #<Metabolite:0x00007f92109e46d0>

OC(=O)C1CC=CC(=N1)C(O)=O
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INCHI for #<Metabolite:0x00007f92109e46d0>

InChI=1S/C7H7NO4/c9-6(10)4-2-1-3-5(8-4)7(11)12/h1-2,5H,3H2,(H,9,10)(H,11,12)
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Synonyms
ValueSource
L-2,3-Dihydrodipicolinic acidGenerator
2,3-Di-H-dipicolinateHMDB
2,3-DihydrodipicolinateHMDB
DihydrodipicolinateHMDB
Molecular FormulaC7H7NO4
Average Mass169.1348
Monoisotopic Mass169.037507717
IUPAC Name2,3-dihydropyridine-2,6-dicarboxylic acid
Traditional Name2,3-dihydrodipicolinic acid
CAS Registry Number16052-12-3
SMILES
OC(=O)C1CC=CC(=N1)C(O)=O
InChI Identifier
InChI=1S/C7H7NO4/c9-6(10)4-2-1-3-5(8-4)7(11)12/h1-2,5H,3H2,(H,9,10)(H,11,12)
InChI KeyUWOCFOFVIBZJGH-UHFFFAOYSA-N