Showing metabocard for (S)-2,3-dihydrodipicolinate (MMDBc0054102)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-06-05 22:53:00 UTC
Update Date2022-09-01 02:27:16 UTC
MiMeDB IDMMDBc0054102
Metabolite Identification
Common Name(S)-2,3-dihydrodipicolinate
Description
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x000055b76bab4078>


  Mrv1533007131514052D          

 13 13  0  0  1  0            999 V2000
   -0.0000    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    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    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
    2.1434   -0.4125    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    0.8250    0.0000 N   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
    2.8579    0.0000    0.0000 O   0  0  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
    1.4289    2.4750    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  5  7  1  1  0  0  0
  8  4  2  0  0  0  0
  8  5  1  0  0  0  0
  9  6  1  0  0  0  0
 10  6  2  0  0  0  0
 11  7  2  0  0  0  0
 12  7  1  0  0  0  0
  5 13  1  6  0  0  0
M  CHG  2   9  -1  12  -1
M  END
Download

3D MOL for #<Metabolite:0x000055b76bab4078>

HMDB0303995
     RDKit          3D
(S)-2,3-dihydrodipicolinate
 17 17  0  0  0  0  0  0  0  0999 V2000
    3.2073   -1.2929    0.7151 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7676   -0.1948    0.3003 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6835    0.7786   -0.0592 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.3325    0.0493    0.1997 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4781   -0.8117    0.5174 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9225   -0.6928    0.4641 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4995   -1.8605   -0.2738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6833   -2.1578   -0.0914 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6987   -2.5622   -1.1272 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.4619    0.5944   -0.0260 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4056    1.5478   -0.3766 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8911    1.3606   -0.2967 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3092   -0.8467    1.5312 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1363    0.4148   -0.9162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1498    1.0164    0.7670 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7125    2.5323   -0.7490 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6192    2.1253   -0.5789 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
  6 13  1  1
 10 14  1  0
 10 15  1  0
 11 16  1  0
 12 17  1  0
M  CHG  2   3  -1   9  -1
M  END
Download

3D SDF for #<Metabolite:0x000055b76bab4078>


  Mrv1533007131514052D          

 13 13  0  0  1  0            999 V2000
   -0.0000    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    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    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
    2.1434   -0.4125    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    0.8250    0.0000 N   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
    2.8579    0.0000    0.0000 O   0  0  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
    1.4289    2.4750    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  5  7  1  1  0  0  0
  8  4  2  0  0  0  0
  8  5  1  0  0  0  0
  9  6  1  0  0  0  0
 10  6  2  0  0  0  0
 11  7  2  0  0  0  0
 12  7  1  0  0  0  0
  5 13  1  6  0  0  0
M  CHG  2   9  -1  12  -1
M  END
> <DATABASE_ID>
MMDBc0054102

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(CC=CC(=N1)C([O-])=O)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)/p-2/t5-/m0/s1

> <INCHI_KEY>
UWOCFOFVIBZJGH-YFKPBYRVSA-L

> <FORMULA>
C7H5NO4

> <MOLECULAR_WEIGHT>
167.121

> <EXACT_MASS>
167.022954805

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
14.164603795829777

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2,3-dihydropyridine-2,6-dicarboxylate

> <ALOGPS_LOGP>
0.10

> <JCHEM_LOGP>
0.661546247

> <ALOGPS_LOGS>
-1.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.9184526200539267

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.170329936807266

> <JCHEM_PKA_STRONGEST_BASIC>
-1.0507329103103564

> <JCHEM_POLAR_SURFACE_AREA>
92.62

> <JCHEM_REFRACTIVITY>
61.0372

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.44e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-2,3-dihydrodipicolinate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x000055b76bab4078>

HMDB0303995
     RDKit          3D
(S)-2,3-dihydrodipicolinate
 17 17  0  0  0  0  0  0  0  0999 V2000
    3.2073   -1.2929    0.7151 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7676   -0.1948    0.3003 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6835    0.7786   -0.0592 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.3325    0.0493    0.1997 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4781   -0.8117    0.5174 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9225   -0.6928    0.4641 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4995   -1.8605   -0.2738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6833   -2.1578   -0.0914 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6987   -2.5622   -1.1272 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.4619    0.5944   -0.0260 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4056    1.5478   -0.3766 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8911    1.3606   -0.2967 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3092   -0.8467    1.5312 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1363    0.4148   -0.9162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1498    1.0164    0.7670 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7125    2.5323   -0.7490 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6192    2.1253   -0.5789 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
  6 13  1  1
 10 14  1  0
 10 15  1  0
 11 16  1  0
 12 17  1  0
M  CHG  2   3  -1   9  -1
M  END
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PDB for #<Metabolite:0x000055b76bab4078>

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      -0.000   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   1.540   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       1.334   2.310   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   3.850   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O-1
HETATM   10  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O-1
HETATM   13  H   UNK     0       2.667   3.080   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6    8                                                  
CONECT    5    3    7    8   13                                             
CONECT    6    4    9   10                                                  
CONECT    7    5   11   12                                                  
CONECT    8    4    5                                                       
CONECT    9    6                                                            
CONECT   10    6                                                            
CONECT   11    7                                                            
CONECT   12    7                                                            
CONECT   13    5                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END
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3D PDB for #<Metabolite:0x000055b76bab4078>

COMPND    HMDB0303995
HETATM    1  O1  UNL     1       3.207  -1.293   0.715  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.768  -0.195   0.300  1.00  0.00           C  
HETATM    3  O2  UNL     1       3.684   0.779  -0.059  1.00  0.00           O1-
HETATM    4  C2  UNL     1       1.332   0.049   0.200  1.00  0.00           C  
HETATM    5  N1  UNL     1       0.478  -0.812   0.517  1.00  0.00           N  
HETATM    6  C3  UNL     1      -0.922  -0.693   0.464  1.00  0.00           C  
HETATM    7  C4  UNL     1      -1.500  -1.860  -0.274  1.00  0.00           C  
HETATM    8  O3  UNL     1      -2.683  -2.158  -0.091  1.00  0.00           O  
HETATM    9  O4  UNL     1      -0.699  -2.562  -1.127  1.00  0.00           O1-
HETATM   10  C5  UNL     1      -1.462   0.594  -0.026  1.00  0.00           C  
HETATM   11  C6  UNL     1      -0.406   1.548  -0.377  1.00  0.00           C  
HETATM   12  C7  UNL     1       0.891   1.361  -0.297  1.00  0.00           C  
HETATM   13  H1  UNL     1      -1.309  -0.847   1.531  1.00  0.00           H  
HETATM   14  H2  UNL     1      -2.136   0.415  -0.916  1.00  0.00           H  
HETATM   15  H3  UNL     1      -2.150   1.016   0.767  1.00  0.00           H  
HETATM   16  H4  UNL     1      -0.712   2.532  -0.749  1.00  0.00           H  
HETATM   17  H5  UNL     1       1.619   2.125  -0.579  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   12   16
CONECT   12   17
END
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SMILES for #<Metabolite:0x000055b76bab4078>

[H][C@]1(CC=CC(=N1)C([O-])=O)C([O-])=O
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INCHI for #<Metabolite:0x000055b76bab4078>

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)/p-2/t5-/m0/s1
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SynonymsNot Available
Chemical FormulaC7H5NO4
Average Molecular Weight167.121
Monoisotopic Molecular Weight167.022954805
IUPAC Name(2S)-2,3-dihydropyridine-2,6-dicarboxylate
Traditional NameL-2,3-dihydrodipicolinate
CAS Registry NumberNot Available
SMILES
[H][C@]1(CC=CC(=N1)C([O-])=O)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)/p-2/t5-/m0/s1
InChI KeyUWOCFOFVIBZJGH-YFKPBYRVSA-L