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Showing metabocard for (S)-2,3-dihydrodipicolinate (HMDB0303995)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 06:16:39 UTC
Update Date2021-09-24 06:16:40 UTC
HMDB IDHMDB0303995
Secondary Accession NumbersNone
Metabolite Identification
Common Name(S)-2,3-dihydrodipicolinate
Description(s)-2,3-dihydrodipicolinate, also known as (S)-2,3-dihydropyridine-2,6-dicarboxylate or 2,3-di-H-dipicolinic acid, 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 (s)-2,3-dihydrodipicolinate is slightly soluble (in water) and a weakly acidic compound (based on its pKa). (s)-2,3-dihydrodipicolinate can be found in a number of food items such as american cranberry, moth bean, parsnip, and giant butterbur, which makes (s)-2,3-dihydrodipicolinate a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0303995 ((S)-2,3-dihydrodipicolinate)


  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 HMDB0303995 ((S)-2,3-dihydrodipicolinate)

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 HMDB0303995 ((S)-2,3-dihydrodipicolinate)


  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>
HMDB0303995

> <DATABASE_NAME>
hmdb

> <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

$$$$
Download

3D-SDF for HMDB0303995 ((S)-2,3-dihydrodipicolinate)

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

PDB for HMDB0303995 ((S)-2,3-dihydrodipicolinate)

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 HMDB0303995 ((S)-2,3-dihydrodipicolinate)

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 HMDB0303995 ((S)-2,3-dihydrodipicolinate)

[H][C@]1(CC=CC(=N1)C([O-])=O)C([O-])=O
Download

INCHI for HMDB0303995 ((S)-2,3-dihydrodipicolinate)

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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View in JSmolView Stereo Labels
Synonyms
ValueSource
(S)-2,3-DihydrodipicolinateChEBI
(S)-2,3-Dihydropyridine-2,6-dicarboxylateChEBI
L-2,3-DihydrodipicolinateChEBI
(S)-2,3-Dihydrodipicolinic acidGenerator
(S)-2,3-Dihydropyridine-2,6-dicarboxylic acidGenerator
L-2,3-Dihydrodipicolinic acidGenerator
(S)-2,3-Dihydrodipicolinic acid(2-)Generator
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
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
  • Dihydropyridinecarboxylic acid derivative
  • Dihydropyridine
  • Dicarboxylic acid or derivatives
  • Hydropyridine
  • Ketimine
  • Carboxylic acid
  • Azacycle
  • Organoheterocyclic compound
  • Organic nitrogen compound
  • Carbonyl group
  • Organonitrogen compound
  • Organooxygen compound
  • Imine
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen 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
PropertyValueSource
logP0.1ALOGPS
logP0.66ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)3.17ChemAxon
pKa (Strongest Basic)-1.1ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area92.62 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity61.04 m³·mol⁻¹ChemAxon
Polarizability14.16 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+135.8232859911
AllCCS[M+H-H2O]+131.35632859911
AllCCS[M+Na]+141.18332859911
AllCCS[M+NH4]+139.98232859911
AllCCS[M-H]-125.61232859911
AllCCS[M+Na-2H]-126.39432859911
AllCCS[M+HCOO]-127.3232859911
DeepCCS[M+H]+131.12730932474
DeepCCS[M-H]-128.72830932474
DeepCCS[M-2H]-163.83730932474
DeepCCS[M+Na]+138.97830932474

Predicted Kovats Retention Indices

Not Available
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 IDFDB030155
KNApSAcK IDNot Available
Chemspider ID4573840
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5460228
PDB IDNot Available
ChEBI ID30620
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