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

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 22:53:00 UTC

Update Date

2022-09-01 02:27:16 UTC

Metabolite ID

MMDBc0054102

Metabolite Identification

Common Name

(S)-2,3-dihydrodipicolinate

Description

(S)-2,3-dihydrodipicolinate(2-), also known as L-2,3-dihydrodipicolinic acid, 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. Based on a literature review very few articles have been published on (S)-2,3-dihydrodipicolinate(2-).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  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

$$$$

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

Synonyms

Value	Source
(S)-2,3-Dihydrodipicolinate	ChEBI
(S)-2,3-Dihydropyridine-2,6-dicarboxylate	ChEBI
L-2,3-Dihydrodipicolinate	ChEBI
(S)-2,3-Dihydrodipicolinic acid	Generator
(S)-2,3-Dihydropyridine-2,6-dicarboxylic acid	Generator
L-2,3-Dihydrodipicolinic acid	Generator
(S)-2,3-Dihydrodipicolinic acid(2-)	Generator

Molecular Formula

C₇H₅NO₄

Average Mass

167.121

Monoisotopic Mass

167.022954805

IUPAC Name

(2S)-2,3-dihydropyridine-2,6-dicarboxylate

Traditional Name

L-2,3-dihydrodipicolinate

CAS Registry Number

Not 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 Key

UWOCFOFVIBZJGH-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.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha 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 Framework

Aliphatic heteromonocyclic compounds

External Descriptors

2,3-dihydrodipicolinate(2-) (CHEBI:30620 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	6.44 g/L	ALOGPS
logP	0.1	ALOGPS
logP	0.66	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	3.17	ChemAxon
pKa (Strongest Basic)	-1.1	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	92.62 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	61.04 m³·mol⁻¹	ChemAxon
Polarizability	14.16 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0016274	(S)-2,3-dihydrodipicolinate	2,6-Pyridinedicarboxylic acid	Dipicolinate synthase subunit A	Synthesis	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Firmicutes	1	Human feces

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

HMDB0303995

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB030155

KNApSAcK ID

Not Available

Chemspider ID

4573840

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5460228

PDB ID

Not Available

ChEBI ID

30620

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

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

MOL for #<Metabolite:0x00007f55b0891bf8>

3D MOL for #<Metabolite:0x00007f55b0891bf8>

3D SDF for #<Metabolite:0x00007f55b0891bf8>

3D-SDF for #<Metabolite:0x00007f55b0891bf8>

PDB for #<Metabolite:0x00007f55b0891bf8>

3D PDB for #<Metabolite:0x00007f55b0891bf8>

SMILES for #<Metabolite:0x00007f55b0891bf8>

INCHI for #<Metabolite:0x00007f55b0891bf8>

Structure for #<Metabolite:0x00007f55b0891bf8>

3D Structure for #<Metabolite:0x00007f55b0891bf8>